Starting phenix.real_space_refine on Fri Sep 19 10:01:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb0_45411/09_2025/9cb0_45411.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb0_45411/09_2025/9cb0_45411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cb0_45411/09_2025/9cb0_45411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb0_45411/09_2025/9cb0_45411.map" model { file = "/net/cci-nas-00/data/ceres_data/9cb0_45411/09_2025/9cb0_45411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb0_45411/09_2025/9cb0_45411.cif" } resolution = 3.1 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= 0.024 sd= 0.529 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 110 5.16 5 C 15453 2.51 5 N 3986 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24229 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7618 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 50, 'TRANS': 925} Chain breaks: 12 Chain: "B" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7992 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 53, 'TRANS': 970} Chain breaks: 9 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8129 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 55, 'TRANS': 985} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.17, per 1000 atoms: 0.25 Number of scatterers: 24229 At special positions: 0 Unit cell: (138.329, 150.186, 179.169, 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 110 16.00 O 4680 8.00 N 3986 7.00 C 15453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.02 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 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.07 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 125 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 24.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.683A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.763A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.782A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.555A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 4.281A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.709A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.671A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.625A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.670A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.664A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.745A pdb=" N VAL B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.054A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.691A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.259A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.035A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.644A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 850 through 857 removed outlier: 3.853A pdb=" N GLY B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.633A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.622A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 940 through 944 removed outlier: 6.849A pdb=" N SER B 943 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 940 through 944' Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.701A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.834A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.576A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 4.263A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.286A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.614A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.618A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.691A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.523A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.502A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.557A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.549A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.680A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.641A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.145A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.013A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.667A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.245A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.744A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.602A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.568A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.547A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 728 removed outlier: 3.527A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.599A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.650A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.066A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.696A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.884A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.603A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.151A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.386A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.514A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.863A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.745A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.297A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.822A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.583A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.651A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.304A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.711A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.597A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.596A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.522A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.590A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.541A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.799A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.786A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1081 through 1083 877 hydrogen bonds defined for protein. 2406 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: 5.58 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 1 1.17 - 1.33: 7066 1.33 - 1.50: 7602 1.50 - 1.66: 9963 1.66 - 1.83: 139 Bond restraints: 24771 Sorted by residual: bond pdb=" CG PRO C 631 " pdb=" CD PRO C 631 " ideal model delta sigma weight residual 1.503 1.006 0.497 3.40e-02 8.65e+02 2.14e+02 bond pdb=" N PRO C 631 " pdb=" CD PRO C 631 " ideal model delta sigma weight residual 1.473 1.573 -0.100 1.40e-02 5.10e+03 5.11e+01 bond pdb=" CB PRO C 631 " pdb=" CG PRO C 631 " ideal model delta sigma weight residual 1.492 1.212 0.280 5.00e-02 4.00e+02 3.13e+01 bond pdb=" C VAL C 130 " pdb=" N CYS C 131 " ideal model delta sigma weight residual 1.327 1.294 0.033 9.40e-03 1.13e+04 1.22e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 24766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 33708 14.76 - 29.53: 1 29.53 - 44.29: 1 44.29 - 59.05: 0 59.05 - 73.81: 1 Bond angle restraints: 33711 Sorted by residual: angle pdb=" CB PRO C 631 " pdb=" CG PRO C 631 " pdb=" CD PRO C 631 " ideal model delta sigma weight residual 106.10 179.91 -73.81 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO C 631 " pdb=" CD PRO C 631 " pdb=" CG PRO C 631 " ideal model delta sigma weight residual 103.20 72.50 30.70 1.50e+00 4.44e-01 4.19e+02 angle pdb=" CA PRO C 631 " pdb=" CB PRO C 631 " pdb=" CG PRO C 631 " ideal model delta sigma weight residual 104.50 77.51 26.99 1.90e+00 2.77e-01 2.02e+02 angle pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" CD PRO A 337 " ideal model delta sigma weight residual 112.00 97.67 14.33 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N PRO A 337 " pdb=" CD PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 103.20 92.93 10.27 1.50e+00 4.44e-01 4.69e+01 ... (remaining 33706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 13717 22.64 - 45.28: 1248 45.28 - 67.93: 185 67.93 - 90.57: 40 90.57 - 113.21: 21 Dihedral angle restraints: 15211 sinusoidal: 6367 harmonic: 8844 Sorted by residual: dihedral pdb=" CA VAL C 622 " pdb=" C VAL C 622 " pdb=" N ALA C 623 " pdb=" CA ALA C 623 " ideal model delta harmonic sigma weight residual -180.00 -129.70 -50.30 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.02 78.02 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -9.67 -76.33 1 1.00e+01 1.00e-02 7.33e+01 ... (remaining 15208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3796 0.108 - 0.217: 144 0.217 - 0.325: 5 0.325 - 0.434: 1 0.434 - 0.542: 2 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 125 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CB VAL C 635 " pdb=" CA VAL C 635 " pdb=" CG1 VAL C 635 " pdb=" CG2 VAL C 635 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 3945 not shown) Planarity restraints: 4333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.079 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 337 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 82 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 166 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C CYS C 166 " 0.063 2.00e-02 2.50e+03 pdb=" O CYS C 166 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 167 " -0.021 2.00e-02 2.50e+03 ... (remaining 4330 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 412 2.66 - 3.22: 21392 3.22 - 3.78: 33566 3.78 - 4.34: 43770 4.34 - 4.90: 75555 Nonbonded interactions: 174695 Sorted by model distance: nonbonded pdb=" NE2 GLN B 134 " pdb=" OG SER B 161 " model vdw 2.096 3.120 nonbonded pdb=" O VAL C 622 " pdb=" N ILE C 624 " model vdw 2.109 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 2.128 3.120 nonbonded pdb=" O ASN B 99 " pdb=" NH1 ARG B 102 " model vdw 2.137 3.120 nonbonded pdb=" NE2 GLN C 493 " pdb=" O SER C 494 " model vdw 2.159 3.120 ... (remaining 174690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 81 or resid 83 through 623 or resid 640 through \ 1304)) selection = (chain 'B' and (resid 27 through 134 or resid 142 through 143 or resid 154 throu \ gh 177 or resid 187 through 413 or resid 418 through 442 or resid 462 through 46 \ 6 or resid 495 through 498 or resid 504 through 526 or resid 529 through 1304)) selection = (chain 'C' and (resid 27 through 81 or resid 83 through 134 or resid 142 through \ 143 or resid 154 through 177 or resid 187 through 413 or resid 418 through 442 \ or resid 462 through 466 or resid 495 through 498 or resid 504 through 526 or re \ sid 529 through 623 or resid 640 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.660 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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 : 0.006 0.497 24844 Z= 0.242 Angle : 0.868 73.813 33892 Z= 0.424 Chirality : 0.051 0.542 3948 Planarity : 0.006 0.110 4307 Dihedral : 17.206 113.211 9395 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.54 % Favored : 93.15 % Rotamer: Outliers : 0.34 % Allowed : 25.61 % Favored : 74.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.07 % 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: -1.00 (0.15), residues: 2980 helix: 2.22 (0.22), residues: 634 sheet: -0.09 (0.20), residues: 703 loop : -2.24 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 102 TYR 0.034 0.002 TYR B 904 PHE 0.015 0.001 PHE B 32 TRP 0.022 0.002 TRP A 633 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00605 (24771) covalent geometry : angle 0.83839 (33711) SS BOND : bond 0.00682 ( 38) SS BOND : angle 3.65922 ( 76) hydrogen bonds : bond 0.23234 ( 874) hydrogen bonds : angle 7.33444 ( 2406) link_BETA1-4 : bond 0.00308 ( 8) link_BETA1-4 : angle 2.58127 ( 24) link_BETA1-6 : bond 0.00560 ( 1) link_BETA1-6 : angle 1.39940 ( 3) link_NAG-ASN : bond 0.00504 ( 26) link_NAG-ASN : angle 2.93842 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 ASN cc_start: 0.8196 (m-40) cc_final: 0.7495 (p0) REVERT: C 132 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6384 (mp0) outliers start: 9 outliers final: 5 residues processed: 257 average time/residue: 0.1898 time to fit residues: 73.6491 Evaluate side-chains 254 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 249 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 239 GLN B 563 GLN B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057154 restraints weight = 74597.500| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.97 r_work: 0.2790 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 24844 Z= 0.139 Angle : 0.663 11.531 33892 Z= 0.342 Chirality : 0.048 0.414 3948 Planarity : 0.005 0.087 4307 Dihedral : 9.954 98.015 3986 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.24 % Favored : 93.52 % Rotamer: Outliers : 2.18 % Allowed : 23.05 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.11 % 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: -0.84 (0.15), residues: 2980 helix: 2.12 (0.21), residues: 662 sheet: 0.18 (0.19), residues: 723 loop : -2.24 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 634 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.001 PHE B1121 TRP 0.022 0.001 TRP B 64 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00290 (24771) covalent geometry : angle 0.64306 (33711) SS BOND : bond 0.00368 ( 38) SS BOND : angle 1.74079 ( 76) hydrogen bonds : bond 0.07365 ( 874) hydrogen bonds : angle 5.55626 ( 2406) link_BETA1-4 : bond 0.00395 ( 8) link_BETA1-4 : angle 2.23740 ( 24) link_BETA1-6 : bond 0.00683 ( 1) link_BETA1-6 : angle 0.93128 ( 3) link_NAG-ASN : bond 0.00466 ( 26) link_NAG-ASN : angle 2.78205 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7697 (t0) cc_final: 0.7494 (t0) REVERT: A 364 ASP cc_start: 0.7378 (t0) cc_final: 0.7150 (t0) REVERT: A 692 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8325 (mm) REVERT: A 1092 GLU cc_start: 0.8552 (pm20) cc_final: 0.8314 (pm20) REVERT: B 104 TRP cc_start: 0.6646 (m-90) cc_final: 0.6394 (m-90) REVERT: B 239 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7640 (tp-100) REVERT: B 1092 GLU cc_start: 0.7870 (pm20) cc_final: 0.7625 (mp0) REVERT: C 196 ASN cc_start: 0.8731 (p0) cc_final: 0.8286 (p0) REVERT: C 448 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7978 (p0) REVERT: C 452 LEU cc_start: 0.7500 (mt) cc_final: 0.7148 (pt) REVERT: C 516 GLU cc_start: 0.8439 (pm20) cc_final: 0.8011 (pm20) REVERT: C 634 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6901 (ttp80) REVERT: C 1031 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7844 (tt0) outliers start: 58 outliers final: 27 residues processed: 310 average time/residue: 0.1868 time to fit residues: 89.0417 Evaluate side-chains 285 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 83 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 134 GLN B 207 HIS B 448 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.073896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.053047 restraints weight = 74946.227| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.97 r_work: 0.2683 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24844 Z= 0.231 Angle : 0.753 11.621 33892 Z= 0.391 Chirality : 0.051 0.419 3948 Planarity : 0.006 0.079 4307 Dihedral : 9.505 94.553 3980 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.45 % Favored : 92.25 % Rotamer: Outliers : 3.69 % Allowed : 23.20 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.12 (0.15), residues: 2980 helix: 1.76 (0.21), residues: 657 sheet: 0.08 (0.19), residues: 712 loop : -2.36 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 646 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.002 PHE B1121 TRP 0.015 0.002 TRP C 436 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00534 (24771) covalent geometry : angle 0.73010 (33711) SS BOND : bond 0.00577 ( 38) SS BOND : angle 2.42252 ( 76) hydrogen bonds : bond 0.09950 ( 874) hydrogen bonds : angle 5.59308 ( 2406) link_BETA1-4 : bond 0.00320 ( 8) link_BETA1-4 : angle 2.17098 ( 24) link_BETA1-6 : bond 0.00510 ( 1) link_BETA1-6 : angle 1.75633 ( 3) link_NAG-ASN : bond 0.00491 ( 26) link_NAG-ASN : angle 2.97365 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 256 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.7584 (t0) cc_final: 0.7212 (t0) REVERT: A 692 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 983 ARG cc_start: 0.9544 (OUTLIER) cc_final: 0.8281 (mtp180) REVERT: A 1092 GLU cc_start: 0.8613 (pm20) cc_final: 0.8362 (pm20) REVERT: B 104 TRP cc_start: 0.6918 (m-90) cc_final: 0.6592 (m-90) REVERT: B 153 MET cc_start: 0.6833 (tpp) cc_final: 0.6089 (tmm) REVERT: B 170 TYR cc_start: 0.8487 (t80) cc_final: 0.8238 (t80) REVERT: B 239 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7733 (tp-100) REVERT: B 448 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7532 (m-40) REVERT: B 498 GLN cc_start: 0.7954 (mp10) cc_final: 0.7513 (mp10) REVERT: B 619 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: B 787 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.8688 (mt0) REVERT: B 1092 GLU cc_start: 0.7864 (pm20) cc_final: 0.7654 (mp0) REVERT: C 132 GLU cc_start: 0.7497 (mp0) cc_final: 0.6836 (mp0) REVERT: C 196 ASN cc_start: 0.8714 (p0) cc_final: 0.8284 (p0) REVERT: C 452 LEU cc_start: 0.7787 (mt) cc_final: 0.7295 (pt) REVERT: C 493 GLN cc_start: 0.8746 (tm-30) cc_final: 0.7918 (tm-30) REVERT: C 515 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: C 516 GLU cc_start: 0.8388 (pm20) cc_final: 0.8023 (pm20) REVERT: C 634 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7127 (ttp80) REVERT: C 658 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8723 (m110) REVERT: C 1031 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8008 (tt0) outliers start: 98 outliers final: 57 residues processed: 335 average time/residue: 0.1747 time to fit residues: 90.1089 Evaluate side-chains 310 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 81 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 448 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055373 restraints weight = 74388.783| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.00 r_work: 0.2745 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24844 Z= 0.149 Angle : 0.662 11.252 33892 Z= 0.340 Chirality : 0.048 0.413 3948 Planarity : 0.005 0.079 4307 Dihedral : 8.971 91.558 3980 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.11 % Favored : 93.62 % Rotamer: Outliers : 3.09 % Allowed : 24.37 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.11 % 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: -0.96 (0.15), residues: 2980 helix: 1.97 (0.21), residues: 658 sheet: 0.21 (0.19), residues: 697 loop : -2.29 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 634 TYR 0.021 0.001 TYR B1138 PHE 0.017 0.001 PHE B 32 TRP 0.019 0.001 TRP A 633 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00314 (24771) covalent geometry : angle 0.64084 (33711) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.99502 ( 76) hydrogen bonds : bond 0.07920 ( 874) hydrogen bonds : angle 5.26765 ( 2406) link_BETA1-4 : bond 0.00311 ( 8) link_BETA1-4 : angle 2.19906 ( 24) link_BETA1-6 : bond 0.00641 ( 1) link_BETA1-6 : angle 1.71405 ( 3) link_NAG-ASN : bond 0.00437 ( 26) link_NAG-ASN : angle 2.74649 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7881 (mmm-85) REVERT: A 364 ASP cc_start: 0.7730 (t0) cc_final: 0.7454 (t0) REVERT: A 692 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 983 ARG cc_start: 0.9521 (OUTLIER) cc_final: 0.8224 (mtp180) REVERT: A 1092 GLU cc_start: 0.8597 (pm20) cc_final: 0.8392 (pm20) REVERT: B 28 TYR cc_start: 0.8806 (m-80) cc_final: 0.8484 (m-10) REVERT: B 97 LYS cc_start: 0.6992 (mmtt) cc_final: 0.6293 (mptt) REVERT: B 104 TRP cc_start: 0.6839 (m-90) cc_final: 0.6456 (m-90) REVERT: B 153 MET cc_start: 0.6871 (tpp) cc_final: 0.5872 (tmm) REVERT: B 170 TYR cc_start: 0.8464 (t80) cc_final: 0.8147 (t80) REVERT: B 239 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7733 (tp-100) REVERT: B 442 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7492 (t0) REVERT: B 1092 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 121 ASN cc_start: 0.6873 (OUTLIER) cc_final: 0.6574 (p0) REVERT: C 196 ASN cc_start: 0.8653 (p0) cc_final: 0.8191 (p0) REVERT: C 409 GLN cc_start: 0.8459 (tt0) cc_final: 0.8225 (tt0) REVERT: C 448 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8015 (p0) REVERT: C 452 LEU cc_start: 0.7684 (mt) cc_final: 0.7223 (pt) REVERT: C 493 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 516 GLU cc_start: 0.8455 (pm20) cc_final: 0.8042 (pm20) REVERT: C 619 GLU cc_start: 0.8764 (tt0) cc_final: 0.8437 (pt0) REVERT: C 1031 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8013 (tt0) outliers start: 82 outliers final: 48 residues processed: 317 average time/residue: 0.1681 time to fit residues: 81.6766 Evaluate side-chains 297 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 237 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054625 restraints weight = 74110.475| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.01 r_work: 0.2726 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24844 Z= 0.169 Angle : 0.683 12.585 33892 Z= 0.350 Chirality : 0.048 0.396 3948 Planarity : 0.005 0.077 4307 Dihedral : 8.742 86.567 3980 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.95 % Favored : 92.82 % Rotamer: Outliers : 3.77 % Allowed : 24.33 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.11 % 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: -0.98 (0.15), residues: 2980 helix: 1.95 (0.21), residues: 658 sheet: 0.22 (0.19), residues: 695 loop : -2.32 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.022 0.002 TYR B1138 PHE 0.019 0.002 PHE B1121 TRP 0.016 0.001 TRP A 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00376 (24771) covalent geometry : angle 0.66130 (33711) SS BOND : bond 0.00445 ( 38) SS BOND : angle 2.15765 ( 76) hydrogen bonds : bond 0.08327 ( 874) hydrogen bonds : angle 5.24022 ( 2406) link_BETA1-4 : bond 0.00304 ( 8) link_BETA1-4 : angle 2.15340 ( 24) link_BETA1-6 : bond 0.00484 ( 1) link_BETA1-6 : angle 1.62574 ( 3) link_NAG-ASN : bond 0.00432 ( 26) link_NAG-ASN : angle 2.76676 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 252 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.7742 (t0) cc_final: 0.7445 (t0) REVERT: A 396 TYR cc_start: 0.8232 (m-10) cc_final: 0.8029 (m-80) REVERT: A 692 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 935 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: A 983 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.8207 (mtp180) REVERT: A 1092 GLU cc_start: 0.8623 (pm20) cc_final: 0.8368 (pm20) REVERT: B 28 TYR cc_start: 0.8834 (m-80) cc_final: 0.8559 (m-10) REVERT: B 104 TRP cc_start: 0.6872 (m-90) cc_final: 0.6543 (m-90) REVERT: B 153 MET cc_start: 0.6884 (tpp) cc_final: 0.5930 (tmm) REVERT: B 170 TYR cc_start: 0.8496 (t80) cc_final: 0.8111 (t80) REVERT: B 239 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7779 (tp-100) REVERT: B 442 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7694 (t0) REVERT: B 1092 GLU cc_start: 0.7944 (pm20) cc_final: 0.7691 (mp0) REVERT: C 121 ASN cc_start: 0.6887 (OUTLIER) cc_final: 0.6636 (p0) REVERT: C 196 ASN cc_start: 0.8639 (p0) cc_final: 0.8182 (p0) REVERT: C 452 LEU cc_start: 0.7736 (mt) cc_final: 0.7301 (pt) REVERT: C 493 GLN cc_start: 0.8634 (tm-30) cc_final: 0.7777 (tm-30) REVERT: C 516 GLU cc_start: 0.8396 (pm20) cc_final: 0.7998 (pm20) REVERT: C 619 GLU cc_start: 0.8797 (tt0) cc_final: 0.8473 (pt0) REVERT: C 658 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (m110) REVERT: C 1031 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8030 (tt0) outliers start: 100 outliers final: 68 residues processed: 333 average time/residue: 0.1753 time to fit residues: 89.9947 Evaluate side-chains 318 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 15 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 394 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054594 restraints weight = 73984.097| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.02 r_work: 0.2726 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24844 Z= 0.168 Angle : 0.687 12.394 33892 Z= 0.352 Chirality : 0.049 0.496 3948 Planarity : 0.005 0.075 4307 Dihedral : 8.513 81.784 3980 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.64 % Favored : 93.15 % Rotamer: Outliers : 4.14 % Allowed : 24.03 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.98 (0.15), residues: 2980 helix: 2.02 (0.21), residues: 651 sheet: 0.20 (0.19), residues: 692 loop : -2.31 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 346 TYR 0.020 0.001 TYR B 351 PHE 0.019 0.002 PHE B1121 TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00374 (24771) covalent geometry : angle 0.66548 (33711) SS BOND : bond 0.00445 ( 38) SS BOND : angle 2.07768 ( 76) hydrogen bonds : bond 0.08292 ( 874) hydrogen bonds : angle 5.19142 ( 2406) link_BETA1-4 : bond 0.00278 ( 8) link_BETA1-4 : angle 2.19401 ( 24) link_BETA1-6 : bond 0.00601 ( 1) link_BETA1-6 : angle 1.57814 ( 3) link_NAG-ASN : bond 0.00428 ( 26) link_NAG-ASN : angle 2.76025 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 246 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.6673 (mmm160) REVERT: A 364 ASP cc_start: 0.7758 (t0) cc_final: 0.7476 (t0) REVERT: A 396 TYR cc_start: 0.8221 (m-10) cc_final: 0.8018 (m-80) REVERT: A 692 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 935 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 983 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.8203 (mtp180) REVERT: A 1092 GLU cc_start: 0.8613 (pm20) cc_final: 0.8373 (pm20) REVERT: B 104 TRP cc_start: 0.6851 (m-90) cc_final: 0.6637 (m-90) REVERT: B 131 CYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7340 (m) REVERT: B 153 MET cc_start: 0.6722 (tpp) cc_final: 0.5813 (tmm) REVERT: B 239 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7772 (tp-100) REVERT: B 241 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7010 (mp) REVERT: B 1092 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 196 ASN cc_start: 0.8649 (p0) cc_final: 0.8169 (p0) REVERT: C 394 ASN cc_start: 0.8202 (t160) cc_final: 0.7945 (t0) REVERT: C 409 GLN cc_start: 0.8510 (tt0) cc_final: 0.8245 (tt0) REVERT: C 452 LEU cc_start: 0.7725 (mt) cc_final: 0.7293 (pt) REVERT: C 493 GLN cc_start: 0.8626 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 516 GLU cc_start: 0.8407 (pm20) cc_final: 0.7956 (pm20) REVERT: C 619 GLU cc_start: 0.8812 (tt0) cc_final: 0.8509 (pt0) REVERT: C 627 ASP cc_start: 0.5969 (t0) cc_final: 0.5736 (t0) REVERT: C 658 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8713 (m110) REVERT: C 1031 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8025 (tt0) outliers start: 110 outliers final: 80 residues processed: 336 average time/residue: 0.1760 time to fit residues: 91.4652 Evaluate side-chains 335 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 246 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 224 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 chunk 215 optimal weight: 0.3980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN C 394 ASN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054358 restraints weight = 74054.990| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.01 r_work: 0.2720 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24844 Z= 0.174 Angle : 0.701 13.358 33892 Z= 0.357 Chirality : 0.048 0.406 3948 Planarity : 0.005 0.076 4307 Dihedral : 8.074 66.705 3980 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.15 % Favored : 92.65 % Rotamer: Outliers : 4.07 % Allowed : 24.41 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.07 % 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: -1.00 (0.15), residues: 2980 helix: 1.94 (0.21), residues: 657 sheet: 0.19 (0.19), residues: 690 loop : -2.31 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 346 TYR 0.025 0.002 TYR B1138 PHE 0.019 0.002 PHE A 92 TRP 0.018 0.001 TRP A 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00389 (24771) covalent geometry : angle 0.67783 (33711) SS BOND : bond 0.00457 ( 38) SS BOND : angle 2.22672 ( 76) hydrogen bonds : bond 0.08439 ( 874) hydrogen bonds : angle 5.20522 ( 2406) link_BETA1-4 : bond 0.00295 ( 8) link_BETA1-4 : angle 2.31320 ( 24) link_BETA1-6 : bond 0.00606 ( 1) link_BETA1-6 : angle 1.57422 ( 3) link_NAG-ASN : bond 0.00440 ( 26) link_NAG-ASN : angle 2.85212 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 252 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8339 (t60) cc_final: 0.8066 (t60) REVERT: A 65 PHE cc_start: 0.8280 (m-10) cc_final: 0.8074 (m-10) REVERT: A 328 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.6689 (mmm160) REVERT: A 364 ASP cc_start: 0.7766 (t0) cc_final: 0.7488 (t0) REVERT: A 692 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 935 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 983 ARG cc_start: 0.9534 (OUTLIER) cc_final: 0.8206 (mtp180) REVERT: A 1092 GLU cc_start: 0.8567 (pm20) cc_final: 0.8331 (pm20) REVERT: B 104 TRP cc_start: 0.6861 (m-90) cc_final: 0.6628 (m-90) REVERT: B 131 CYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7311 (m) REVERT: B 153 MET cc_start: 0.6650 (tpp) cc_final: 0.5740 (tmm) REVERT: B 239 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7742 (tp-100) REVERT: B 241 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7047 (mp) REVERT: B 1092 GLU cc_start: 0.7908 (pm20) cc_final: 0.7661 (mp0) REVERT: C 132 GLU cc_start: 0.7564 (mp0) cc_final: 0.7306 (mp0) REVERT: C 196 ASN cc_start: 0.8621 (p0) cc_final: 0.8139 (p0) REVERT: C 409 GLN cc_start: 0.8491 (tt0) cc_final: 0.8147 (tt0) REVERT: C 452 LEU cc_start: 0.7739 (mt) cc_final: 0.7310 (pt) REVERT: C 493 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7694 (tm-30) REVERT: C 516 GLU cc_start: 0.8400 (pm20) cc_final: 0.7995 (pm20) REVERT: C 619 GLU cc_start: 0.8825 (tt0) cc_final: 0.8611 (pt0) REVERT: C 658 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8713 (m110) REVERT: C 1031 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8047 (tt0) outliers start: 108 outliers final: 89 residues processed: 342 average time/residue: 0.1585 time to fit residues: 84.2956 Evaluate side-chains 345 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 248 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 27 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 234 optimal weight: 0.0670 chunk 238 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.0010 overall best weight: 0.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 134 GLN C 394 ASN C 448 ASN C 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.057264 restraints weight = 74098.881| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.97 r_work: 0.2798 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24844 Z= 0.130 Angle : 0.646 14.067 33892 Z= 0.329 Chirality : 0.047 0.380 3948 Planarity : 0.005 0.069 4307 Dihedral : 7.322 59.899 3980 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.67 % Favored : 94.13 % Rotamer: Outliers : 3.09 % Allowed : 25.76 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.07 % 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: -0.77 (0.15), residues: 2980 helix: 2.20 (0.21), residues: 656 sheet: 0.28 (0.19), residues: 722 loop : -2.21 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 346 TYR 0.029 0.001 TYR A 396 PHE 0.018 0.001 PHE A 374 TRP 0.023 0.001 TRP A 633 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00270 (24771) covalent geometry : angle 0.62310 (33711) SS BOND : bond 0.00536 ( 38) SS BOND : angle 1.74357 ( 76) hydrogen bonds : bond 0.06696 ( 874) hydrogen bonds : angle 4.94209 ( 2406) link_BETA1-4 : bond 0.00353 ( 8) link_BETA1-4 : angle 2.39900 ( 24) link_BETA1-6 : bond 0.00685 ( 1) link_BETA1-6 : angle 1.32912 ( 3) link_NAG-ASN : bond 0.00507 ( 26) link_NAG-ASN : angle 2.99402 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 267 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8284 (t60) cc_final: 0.8035 (t60) REVERT: A 324 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6662 (tm-30) REVERT: A 364 ASP cc_start: 0.7859 (t0) cc_final: 0.7628 (t0) REVERT: A 692 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 935 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 983 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.8316 (mtp180) REVERT: A 1092 GLU cc_start: 0.8479 (pm20) cc_final: 0.8268 (pm20) REVERT: B 32 PHE cc_start: 0.8351 (m-80) cc_final: 0.7963 (m-80) REVERT: B 104 TRP cc_start: 0.6649 (m-90) cc_final: 0.6313 (m-90) REVERT: B 127 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8351 (m) REVERT: B 131 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7256 (m) REVERT: B 170 TYR cc_start: 0.8506 (t80) cc_final: 0.8031 (t80) REVERT: C 196 ASN cc_start: 0.8594 (p0) cc_final: 0.8101 (p0) REVERT: C 448 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8201 (p0) REVERT: C 452 LEU cc_start: 0.7724 (mt) cc_final: 0.7321 (pt) REVERT: C 493 GLN cc_start: 0.8653 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 516 GLU cc_start: 0.8379 (pm20) cc_final: 0.7978 (pm20) REVERT: C 1031 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7898 (tt0) outliers start: 82 outliers final: 61 residues processed: 331 average time/residue: 0.1733 time to fit residues: 89.1184 Evaluate side-chains 319 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 292 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.076815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056084 restraints weight = 74451.360| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.97 r_work: 0.2769 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24844 Z= 0.149 Angle : 0.673 11.058 33892 Z= 0.345 Chirality : 0.047 0.377 3948 Planarity : 0.005 0.075 4307 Dihedral : 7.099 58.895 3980 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.51 % Favored : 93.26 % Rotamer: Outliers : 3.16 % Allowed : 26.03 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.07 % 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: -0.78 (0.15), residues: 2980 helix: 2.21 (0.21), residues: 654 sheet: 0.29 (0.19), residues: 716 loop : -2.23 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 346 TYR 0.019 0.001 TYR B 351 PHE 0.026 0.001 PHE A 92 TRP 0.022 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00326 (24771) covalent geometry : angle 0.65324 (33711) SS BOND : bond 0.00393 ( 38) SS BOND : angle 2.02278 ( 76) hydrogen bonds : bond 0.07265 ( 874) hydrogen bonds : angle 4.96107 ( 2406) link_BETA1-4 : bond 0.00266 ( 8) link_BETA1-4 : angle 2.04120 ( 24) link_BETA1-6 : bond 0.00516 ( 1) link_BETA1-6 : angle 1.44457 ( 3) link_NAG-ASN : bond 0.00442 ( 26) link_NAG-ASN : angle 2.67080 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 252 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8311 (t60) cc_final: 0.8059 (t60) REVERT: A 102 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: A 324 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6715 (tm-30) REVERT: A 364 ASP cc_start: 0.7891 (t0) cc_final: 0.7657 (t0) REVERT: A 692 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 935 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: A 983 ARG cc_start: 0.9539 (OUTLIER) cc_final: 0.8331 (mtp180) REVERT: A 1092 GLU cc_start: 0.8491 (pm20) cc_final: 0.8263 (pm20) REVERT: B 32 PHE cc_start: 0.8418 (m-80) cc_final: 0.8045 (m-80) REVERT: B 92 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: B 104 TRP cc_start: 0.6733 (m-90) cc_final: 0.6357 (m-90) REVERT: B 127 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 131 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7084 (m) REVERT: B 277 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8739 (mt) REVERT: B 493 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7080 (mm-40) REVERT: C 165 ASN cc_start: 0.8461 (t0) cc_final: 0.8101 (t0) REVERT: C 196 ASN cc_start: 0.8587 (p0) cc_final: 0.8102 (p0) REVERT: C 406 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: C 409 GLN cc_start: 0.7971 (tt0) cc_final: 0.7581 (tt0) REVERT: C 452 LEU cc_start: 0.7751 (mt) cc_final: 0.7340 (pt) REVERT: C 493 GLN cc_start: 0.8654 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 516 GLU cc_start: 0.8334 (pm20) cc_final: 0.7971 (pm20) REVERT: C 1031 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7901 (tt0) outliers start: 84 outliers final: 73 residues processed: 320 average time/residue: 0.1773 time to fit residues: 87.0438 Evaluate side-chains 333 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 251 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 207 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 272 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057467 restraints weight = 74598.006| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.98 r_work: 0.2804 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24844 Z= 0.131 Angle : 0.651 11.064 33892 Z= 0.333 Chirality : 0.046 0.375 3948 Planarity : 0.005 0.070 4307 Dihedral : 6.857 59.468 3980 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 2.94 % Allowed : 26.40 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.69 (0.15), residues: 2980 helix: 2.33 (0.21), residues: 655 sheet: 0.29 (0.19), residues: 737 loop : -2.19 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 346 TYR 0.022 0.001 TYR C 160 PHE 0.014 0.001 PHE B 135 TRP 0.038 0.002 TRP A 633 HIS 0.002 0.000 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00277 (24771) covalent geometry : angle 0.63363 (33711) SS BOND : bond 0.00363 ( 38) SS BOND : angle 1.81486 ( 76) hydrogen bonds : bond 0.06520 ( 874) hydrogen bonds : angle 4.86926 ( 2406) link_BETA1-4 : bond 0.00375 ( 8) link_BETA1-4 : angle 1.95156 ( 24) link_BETA1-6 : bond 0.00493 ( 1) link_BETA1-6 : angle 1.31114 ( 3) link_NAG-ASN : bond 0.00437 ( 26) link_NAG-ASN : angle 2.52829 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8311 (t60) cc_final: 0.8044 (t60) REVERT: A 102 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: A 324 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 364 ASP cc_start: 0.7875 (t0) cc_final: 0.7656 (t0) REVERT: A 692 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 935 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: A 1092 GLU cc_start: 0.8480 (pm20) cc_final: 0.8271 (pm20) REVERT: B 32 PHE cc_start: 0.8402 (m-80) cc_final: 0.8052 (m-80) REVERT: B 92 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: B 104 TRP cc_start: 0.6617 (m-90) cc_final: 0.6201 (m-90) REVERT: B 127 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 131 CYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6492 (m) REVERT: B 277 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8721 (mt) REVERT: B 462 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8672 (tmtt) REVERT: B 493 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6610 (mp10) REVERT: C 196 ASN cc_start: 0.8611 (p0) cc_final: 0.8143 (p0) REVERT: C 452 LEU cc_start: 0.7731 (mt) cc_final: 0.7340 (pt) REVERT: C 493 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 516 GLU cc_start: 0.8333 (pm20) cc_final: 0.7953 (pm20) REVERT: C 1031 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7840 (tt0) outliers start: 78 outliers final: 69 residues processed: 319 average time/residue: 0.1641 time to fit residues: 81.7458 Evaluate side-chains 326 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 250 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 78 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057036 restraints weight = 74213.477| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.97 r_work: 0.2790 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24844 Z= 0.137 Angle : 0.658 10.968 33892 Z= 0.337 Chirality : 0.047 0.370 3948 Planarity : 0.005 0.074 4307 Dihedral : 6.688 58.835 3980 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.54 % Favored : 93.26 % Rotamer: Outliers : 3.13 % Allowed : 26.33 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.07 % 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: -0.69 (0.15), residues: 2980 helix: 2.33 (0.21), residues: 655 sheet: 0.37 (0.19), residues: 722 loop : -2.21 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 634 TYR 0.023 0.001 TYR B1138 PHE 0.026 0.001 PHE A 92 TRP 0.029 0.001 TRP A 633 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00296 (24771) covalent geometry : angle 0.64047 (33711) SS BOND : bond 0.00361 ( 38) SS BOND : angle 1.86655 ( 76) hydrogen bonds : bond 0.06740 ( 874) hydrogen bonds : angle 4.85126 ( 2406) link_BETA1-4 : bond 0.00226 ( 8) link_BETA1-4 : angle 1.85807 ( 24) link_BETA1-6 : bond 0.00483 ( 1) link_BETA1-6 : angle 1.33057 ( 3) link_NAG-ASN : bond 0.00427 ( 26) link_NAG-ASN : angle 2.51253 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5712.36 seconds wall clock time: 98 minutes 35.39 seconds (5915.39 seconds total)