Starting phenix.real_space_refine on Mon Aug 25 05:31:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xm3_22254/08_2025/6xm3_22254.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xm3_22254/08_2025/6xm3_22254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xm3_22254/08_2025/6xm3_22254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xm3_22254/08_2025/6xm3_22254.map" model { file = "/net/cci-nas-00/data/ceres_data/6xm3_22254/08_2025/6xm3_22254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xm3_22254/08_2025/6xm3_22254.cif" } resolution = 2.9 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= -0.000 sd= 0.965 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 16148 2.51 5 N 4142 2.21 5 O 4984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25384 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8111 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain breaks: 7 Chain: "B" Number of atoms: 8259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 bond proxies already assigned to first conformer: 8435 Chain: "C" Number of atoms: 8174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8174 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 52, 'TRANS': 994} 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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: "C" 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 Time building chain proxies: 7.33, per 1000 atoms: 0.29 Number of scatterers: 25384 At special positions: 0 Unit cell: (140.25, 136, 199.75, 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 4984 8.00 N 4142 7.00 C 16148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 44 sheets defined 24.2% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.503A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.613A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.686A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.698A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.569A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.741A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.896A 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 removed outlier: 3.557A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.559A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.560A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.979A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.603A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.511A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.605A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.733A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.605A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.684A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.747A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.565A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.632A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.509A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 806 Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 839 removed outlier: 3.554A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.636A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.762A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.655A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 935 removed outlier: 3.513A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.605A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.135A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.553A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.124A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.891A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.522A 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 619 through 624 Processing helix chain 'C' and resid 625 through 629 removed outlier: 4.018A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.610A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.636A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 removed outlier: 3.637A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 removed outlier: 3.545A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.531A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.803A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.691A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.611A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (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 982 Processing helix chain 'C' and resid 985 through 989 Processing helix chain 'C' and resid 992 through 1032 removed outlier: 3.754A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.014A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.866A 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: 6.439A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.256A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.671A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 3.978A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.585A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.834A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.012A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.391A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.470A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.210A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.860A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.295A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.001A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.657A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.744A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.684A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.021A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.790A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.535A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.669A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.679A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.066A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.795A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.545A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.640A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.544A 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 728 removed outlier: 6.609A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.609A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 836 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7554 1.33 - 1.46: 7080 1.46 - 1.60: 11176 1.60 - 1.73: 1 1.73 - 1.86: 134 Bond restraints: 25945 Sorted by residual: bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.20e-02 6.94e+03 1.39e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.201 0.040 1.12e-02 7.97e+03 1.26e+01 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.06e-02 8.90e+03 1.18e+01 bond pdb=" C LYS B 790 " pdb=" N THR B 791 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.03e+01 bond pdb=" C ASP B 808 " pdb=" N PRO B 809 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.06e-02 8.90e+03 9.79e+00 ... (remaining 25940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 34462 2.80 - 5.59: 762 5.59 - 8.39: 73 8.39 - 11.18: 19 11.18 - 13.98: 5 Bond angle restraints: 35321 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.30 99.46 13.84 1.34e+00 5.57e-01 1.07e+02 angle pdb=" C ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta sigma weight residual 109.83 119.71 -9.88 9.90e-01 1.02e+00 9.95e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.23e+00 6.61e-01 5.56e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 angle pdb=" CA VAL B 620 " pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 120.83 124.32 -3.49 6.10e-01 2.69e+00 3.28e+01 ... (remaining 35316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 14512 17.50 - 35.00: 1324 35.00 - 52.50: 304 52.50 - 70.00: 64 70.00 - 87.49: 31 Dihedral angle restraints: 16235 sinusoidal: 7074 harmonic: 9161 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 176.60 -83.60 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 161.11 -68.11 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -30.58 -55.42 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 16232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3527 0.095 - 0.189: 614 0.189 - 0.284: 49 0.284 - 0.378: 4 0.378 - 0.473: 6 Chirality restraints: 4200 Sorted by residual: chirality pdb=" CA ASN B 616 " pdb=" N ASN B 616 " pdb=" C ASN B 616 " pdb=" CB ASN B 616 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 4197 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 987 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 393 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C THR A 393 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 393 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 394 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.020 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE C 906 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.002 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5127 2.77 - 3.30: 20566 3.30 - 3.83: 39415 3.83 - 4.37: 46372 4.37 - 4.90: 82677 Nonbonded interactions: 194157 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.233 3.040 nonbonded pdb=" O GLN A 134 " pdb=" OH TYR A 160 " model vdw 2.252 3.040 nonbonded pdb=" O LEU B 293 " pdb=" OG1 THR B 632 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.265 3.040 nonbonded pdb=" O GLN C 134 " pdb=" OH TYR C 160 " model vdw 2.266 3.040 ... (remaining 194152 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 172 or resid 186 through 250 or resid 265 throu \ gh 492 or resid 494 through 848 or resid 850 through 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 444 or resid 447 throu \ gh 492 or resid 494 through 828 or resid 848 or resid 850 through 1308)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 492 or resid 494 throu \ gh 828 or resid 830 or resid 834 or resid 851 through 1308)) } 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 8.320 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.280 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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:9.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.012 0.137 26046 Z= 0.537 Angle : 1.061 13.975 35583 Z= 0.577 Chirality : 0.071 0.473 4200 Planarity : 0.008 0.104 4493 Dihedral : 14.378 87.494 10214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 0.66 % Allowed : 6.37 % Favored : 92.97 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.38 (0.12), residues: 3100 helix: -4.55 (0.08), residues: 672 sheet: -1.28 (0.19), residues: 705 loop : -3.00 (0.12), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.034 0.003 TYR B 904 PHE 0.054 0.003 PHE C 906 TRP 0.043 0.003 TRP A 886 HIS 0.011 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01251 (25945) covalent geometry : angle 1.03475 (35321) SS BOND : bond 0.00782 ( 41) SS BOND : angle 2.90747 ( 82) hydrogen bonds : bond 0.31068 ( 810) hydrogen bonds : angle 9.95275 ( 2250) link_BETA1-4 : bond 0.00875 ( 17) link_BETA1-4 : angle 2.16118 ( 51) link_NAG-ASN : bond 0.00732 ( 43) link_NAG-ASN : angle 3.21469 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6850 (mtmm) REVERT: A 351 TYR cc_start: 0.8090 (p90) cc_final: 0.7682 (p90) REVERT: A 365 TYR cc_start: 0.8053 (m-80) cc_final: 0.7734 (m-80) REVERT: A 378 LYS cc_start: 0.7585 (tttm) cc_final: 0.6897 (tmtt) REVERT: A 385 THR cc_start: 0.8488 (m) cc_final: 0.8245 (p) REVERT: A 403 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7292 (ttm-80) REVERT: A 417 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7343 (mtpt) REVERT: A 420 ASP cc_start: 0.7937 (m-30) cc_final: 0.7542 (m-30) REVERT: A 505 TYR cc_start: 0.7701 (m-80) cc_final: 0.7478 (m-80) REVERT: A 773 GLU cc_start: 0.8145 (tt0) cc_final: 0.7767 (tt0) REVERT: A 904 TYR cc_start: 0.7612 (m-80) cc_final: 0.7233 (m-80) REVERT: A 1086 LYS cc_start: 0.8406 (mmpt) cc_final: 0.8136 (mtpt) REVERT: B 218 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8170 (mm-40) REVERT: B 396 TYR cc_start: 0.7445 (m-80) cc_final: 0.7039 (m-80) REVERT: B 613 GLN cc_start: 0.7621 (mt0) cc_final: 0.6962 (pt0) REVERT: B 635 VAL cc_start: 0.8125 (t) cc_final: 0.7832 (m) REVERT: B 850 ILE cc_start: 0.8167 (mp) cc_final: 0.7796 (mm) REVERT: B 1125 ASN cc_start: 0.7939 (m-40) cc_final: 0.7585 (t0) REVERT: B 1138 TYR cc_start: 0.7816 (t80) cc_final: 0.7516 (t80) REVERT: C 190 ARG cc_start: 0.5823 (mtt-85) cc_final: 0.4879 (ttp-170) REVERT: C 273 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7208 (mmt-90) REVERT: C 319 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7658 (ttm110) REVERT: C 357 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7648 (ttt-90) REVERT: C 430 THR cc_start: 0.8416 (t) cc_final: 0.8210 (m) REVERT: C 603 ASN cc_start: 0.8640 (t0) cc_final: 0.8364 (t0) REVERT: C 1092 GLU cc_start: 0.7289 (mp0) cc_final: 0.6869 (pp20) outliers start: 16 outliers final: 6 residues processed: 267 average time/residue: 0.6253 time to fit residues: 194.2303 Evaluate side-chains 181 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 439 ASN A 787 GLN A 901 GLN A 954 GLN B 30 ASN B 134 GLN B 137 ASN B 211 ASN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 556 ASN B 675 GLN B 901 GLN C 87 ASN C 211 ASN C 314 GLN C 564 GLN C 613 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107953 restraints weight = 34300.821| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.38 r_work: 0.3044 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 26046 Z= 0.128 Angle : 0.665 23.896 35583 Z= 0.338 Chirality : 0.047 0.314 4200 Planarity : 0.005 0.076 4493 Dihedral : 7.797 59.950 4633 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.68 % Allowed : 9.98 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.13), residues: 3100 helix: -2.19 (0.17), residues: 675 sheet: -0.55 (0.20), residues: 658 loop : -2.45 (0.12), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.027 0.001 TYR B 904 PHE 0.020 0.001 PHE B 377 TRP 0.018 0.002 TRP A 886 HIS 0.004 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00285 (25945) covalent geometry : angle 0.64745 (35321) SS BOND : bond 0.00369 ( 41) SS BOND : angle 1.65596 ( 82) hydrogen bonds : bond 0.06097 ( 810) hydrogen bonds : angle 5.87890 ( 2250) link_BETA1-4 : bond 0.00343 ( 17) link_BETA1-4 : angle 1.19858 ( 51) link_NAG-ASN : bond 0.00344 ( 43) link_NAG-ASN : angle 2.17586 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6846 (pt0) cc_final: 0.6630 (pp20) REVERT: A 129 LYS cc_start: 0.7357 (mtpp) cc_final: 0.7024 (mtmm) REVERT: A 351 TYR cc_start: 0.8246 (p90) cc_final: 0.7919 (p90) REVERT: A 403 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7656 (ttm-80) REVERT: A 417 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7472 (mtpt) REVERT: A 420 ASP cc_start: 0.8283 (m-30) cc_final: 0.7973 (m-30) REVERT: A 462 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7894 (mppt) REVERT: A 505 TYR cc_start: 0.7731 (m-80) cc_final: 0.7530 (m-80) REVERT: A 563 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.4861 (mp10) REVERT: A 773 GLU cc_start: 0.8744 (tt0) cc_final: 0.8391 (tt0) REVERT: A 1086 LYS cc_start: 0.8481 (mmpt) cc_final: 0.8174 (mtpt) REVERT: B 396 TYR cc_start: 0.7465 (m-80) cc_final: 0.7040 (m-80) REVERT: B 613 GLN cc_start: 0.7990 (mt0) cc_final: 0.7448 (pt0) REVERT: B 635 VAL cc_start: 0.8293 (t) cc_final: 0.8017 (m) REVERT: B 826 VAL cc_start: 0.9071 (p) cc_final: 0.8628 (t) REVERT: B 850 ILE cc_start: 0.7861 (mp) cc_final: 0.7562 (mm) REVERT: B 988 GLU cc_start: 0.7964 (mp0) cc_final: 0.7292 (mp0) REVERT: B 1125 ASN cc_start: 0.8196 (m-40) cc_final: 0.7641 (t0) REVERT: B 1138 TYR cc_start: 0.8089 (t80) cc_final: 0.7848 (t80) REVERT: C 205 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8974 (t) REVERT: C 314 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8216 (tp-100) REVERT: C 505 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: C 603 ASN cc_start: 0.8805 (t0) cc_final: 0.8564 (t0) REVERT: C 646 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7952 (mtp180) outliers start: 44 outliers final: 11 residues processed: 235 average time/residue: 0.6029 time to fit residues: 166.1800 Evaluate side-chains 193 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 217 optimal weight: 0.4980 chunk 230 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107206 restraints weight = 36763.835| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.80 r_work: 0.3010 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26046 Z= 0.130 Angle : 0.627 21.728 35583 Z= 0.316 Chirality : 0.046 0.280 4200 Planarity : 0.005 0.066 4493 Dihedral : 7.010 59.319 4627 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.00 % Allowed : 11.51 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.14), residues: 3100 helix: -0.92 (0.20), residues: 674 sheet: -0.18 (0.20), residues: 657 loop : -2.24 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.030 0.001 TYR B 904 PHE 0.016 0.001 PHE C 32 TRP 0.014 0.001 TRP B 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00308 (25945) covalent geometry : angle 0.60953 (35321) SS BOND : bond 0.00326 ( 41) SS BOND : angle 1.77542 ( 82) hydrogen bonds : bond 0.05478 ( 810) hydrogen bonds : angle 5.42018 ( 2250) link_BETA1-4 : bond 0.00368 ( 17) link_BETA1-4 : angle 1.24222 ( 51) link_NAG-ASN : bond 0.00288 ( 43) link_NAG-ASN : angle 1.99389 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6919 (pt0) cc_final: 0.6634 (pp20) REVERT: A 351 TYR cc_start: 0.8289 (p90) cc_final: 0.7993 (p90) REVERT: A 417 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7529 (mtpt) REVERT: A 420 ASP cc_start: 0.8301 (m-30) cc_final: 0.7923 (m-30) REVERT: A 462 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7785 (mppt) REVERT: A 563 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.4869 (mp10) REVERT: A 773 GLU cc_start: 0.8829 (tt0) cc_final: 0.8459 (tt0) REVERT: A 1086 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8116 (mtpt) REVERT: B 396 TYR cc_start: 0.7504 (m-80) cc_final: 0.7129 (m-80) REVERT: B 613 GLN cc_start: 0.8054 (mt0) cc_final: 0.7486 (pt0) REVERT: B 635 VAL cc_start: 0.8250 (t) cc_final: 0.8001 (m) REVERT: B 826 VAL cc_start: 0.9082 (p) cc_final: 0.8616 (t) REVERT: B 850 ILE cc_start: 0.7803 (mp) cc_final: 0.7483 (mm) REVERT: B 1118 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (t70) REVERT: B 1125 ASN cc_start: 0.8198 (m-40) cc_final: 0.7632 (t0) REVERT: B 1138 TYR cc_start: 0.8127 (t80) cc_final: 0.7894 (t80) REVERT: C 205 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8989 (t) REVERT: C 505 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: C 561 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8797 (t0) cc_final: 0.8577 (t0) REVERT: C 748 GLU cc_start: 0.8398 (tp30) cc_final: 0.8121 (tp30) outliers start: 53 outliers final: 22 residues processed: 218 average time/residue: 0.4394 time to fit residues: 113.5524 Evaluate side-chains 201 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 145 optimal weight: 0.0570 chunk 96 optimal weight: 0.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 314 GLN C 755 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108944 restraints weight = 36399.466| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.69 r_work: 0.2998 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26046 Z= 0.150 Angle : 0.629 19.213 35583 Z= 0.317 Chirality : 0.047 0.262 4200 Planarity : 0.004 0.062 4493 Dihedral : 6.537 57.690 4627 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.55 % Allowed : 11.73 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.14), residues: 3100 helix: -0.35 (0.20), residues: 682 sheet: -0.06 (0.20), residues: 671 loop : -2.15 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 509 TYR 0.025 0.001 TYR B 904 PHE 0.018 0.001 PHE A 592 TRP 0.038 0.002 TRP B 436 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00365 (25945) covalent geometry : angle 0.61359 (35321) SS BOND : bond 0.00369 ( 41) SS BOND : angle 1.56575 ( 82) hydrogen bonds : bond 0.05476 ( 810) hydrogen bonds : angle 5.24460 ( 2250) link_BETA1-4 : bond 0.00361 ( 17) link_BETA1-4 : angle 1.27967 ( 51) link_NAG-ASN : bond 0.00288 ( 43) link_NAG-ASN : angle 1.93719 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7568 (mtpt) REVERT: A 420 ASP cc_start: 0.8296 (m-30) cc_final: 0.7842 (m-30) REVERT: A 466 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7647 (ttt-90) REVERT: A 563 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.4899 (mp10) REVERT: A 773 GLU cc_start: 0.8840 (tt0) cc_final: 0.8421 (tt0) REVERT: B 396 TYR cc_start: 0.7478 (m-80) cc_final: 0.7110 (m-80) REVERT: B 436 TRP cc_start: 0.5565 (p90) cc_final: 0.5340 (p-90) REVERT: B 613 GLN cc_start: 0.8128 (mt0) cc_final: 0.7530 (pt0) REVERT: B 635 VAL cc_start: 0.8328 (t) cc_final: 0.8069 (m) REVERT: B 826 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8641 (t) REVERT: B 850 ILE cc_start: 0.7772 (mp) cc_final: 0.7455 (mm) REVERT: B 1118 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8082 (t70) REVERT: B 1125 ASN cc_start: 0.8213 (m-40) cc_final: 0.7681 (t0) REVERT: C 505 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6095 (m-80) REVERT: C 561 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8226 (Cg_endo) REVERT: C 603 ASN cc_start: 0.8809 (t0) cc_final: 0.8605 (t0) REVERT: C 748 GLU cc_start: 0.8492 (tp30) cc_final: 0.8149 (tp30) outliers start: 68 outliers final: 30 residues processed: 238 average time/residue: 0.4844 time to fit residues: 137.6562 Evaluate side-chains 207 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 3 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 268 optimal weight: 0.4980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN C 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104818 restraints weight = 40494.860| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.02 r_work: 0.2923 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26046 Z= 0.202 Angle : 0.683 19.423 35583 Z= 0.343 Chirality : 0.050 0.273 4200 Planarity : 0.005 0.060 4493 Dihedral : 6.578 56.814 4627 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.48 % Allowed : 12.75 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.14), residues: 3100 helix: -0.30 (0.20), residues: 687 sheet: 0.00 (0.20), residues: 667 loop : -2.13 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.023 0.002 TYR B 904 PHE 0.024 0.002 PHE B 392 TRP 0.022 0.002 TRP B 436 HIS 0.009 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00505 (25945) covalent geometry : angle 0.66378 (35321) SS BOND : bond 0.00424 ( 41) SS BOND : angle 2.26803 ( 82) hydrogen bonds : bond 0.06057 ( 810) hydrogen bonds : angle 5.32889 ( 2250) link_BETA1-4 : bond 0.00413 ( 17) link_BETA1-4 : angle 1.38258 ( 51) link_NAG-ASN : bond 0.00307 ( 43) link_NAG-ASN : angle 2.01151 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7597 (mtpt) REVERT: A 420 ASP cc_start: 0.8160 (m-30) cc_final: 0.7685 (m-30) REVERT: A 563 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.5008 (mp10) REVERT: A 773 GLU cc_start: 0.8719 (tt0) cc_final: 0.8329 (tt0) REVERT: B 396 TYR cc_start: 0.7487 (m-80) cc_final: 0.7212 (m-80) REVERT: B 613 GLN cc_start: 0.8045 (mt0) cc_final: 0.7479 (pt0) REVERT: B 635 VAL cc_start: 0.8417 (t) cc_final: 0.8164 (m) REVERT: B 826 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 850 ILE cc_start: 0.7919 (mp) cc_final: 0.7561 (mm) REVERT: B 1118 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8001 (t70) REVERT: B 1125 ASN cc_start: 0.8194 (m-40) cc_final: 0.7745 (t0) REVERT: C 129 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5615 (mttt) REVERT: C 239 GLN cc_start: 0.8324 (pt0) cc_final: 0.7986 (pt0) REVERT: C 505 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.5995 (m-80) REVERT: C 748 GLU cc_start: 0.8338 (tp30) cc_final: 0.8014 (tp30) outliers start: 66 outliers final: 37 residues processed: 216 average time/residue: 0.4647 time to fit residues: 118.8245 Evaluate side-chains 205 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 275 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 169 optimal weight: 0.0040 chunk 112 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 143 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109417 restraints weight = 47992.083| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.95 r_work: 0.3002 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26046 Z= 0.129 Angle : 0.610 17.861 35583 Z= 0.308 Chirality : 0.047 0.278 4200 Planarity : 0.004 0.059 4493 Dihedral : 6.147 57.442 4627 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.33 % Allowed : 13.77 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3100 helix: 0.12 (0.21), residues: 679 sheet: 0.22 (0.20), residues: 666 loop : -2.05 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.019 0.001 TYR B 904 PHE 0.028 0.001 PHE B 392 TRP 0.027 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00312 (25945) covalent geometry : angle 0.59323 (35321) SS BOND : bond 0.00284 ( 41) SS BOND : angle 1.84610 ( 82) hydrogen bonds : bond 0.04912 ( 810) hydrogen bonds : angle 5.09569 ( 2250) link_BETA1-4 : bond 0.00367 ( 17) link_BETA1-4 : angle 1.23466 ( 51) link_NAG-ASN : bond 0.00258 ( 43) link_NAG-ASN : angle 1.90344 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7732 (mtpt) REVERT: A 420 ASP cc_start: 0.8286 (m-30) cc_final: 0.7897 (m-30) REVERT: A 558 LYS cc_start: 0.6592 (mmtm) cc_final: 0.6385 (mmtt) REVERT: A 563 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.5026 (mp10) REVERT: A 773 GLU cc_start: 0.8867 (tt0) cc_final: 0.8467 (tt0) REVERT: A 1086 LYS cc_start: 0.8575 (mmpt) cc_final: 0.8238 (mppt) REVERT: B 396 TYR cc_start: 0.7455 (m-80) cc_final: 0.7162 (m-80) REVERT: B 581 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6712 (p) REVERT: B 613 GLN cc_start: 0.8159 (mt0) cc_final: 0.7569 (pt0) REVERT: B 826 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8629 (t) REVERT: B 850 ILE cc_start: 0.7897 (mp) cc_final: 0.7562 (mm) REVERT: B 1118 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8203 (t70) REVERT: B 1125 ASN cc_start: 0.8217 (m-40) cc_final: 0.7747 (t0) REVERT: C 129 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5735 (mttt) REVERT: C 271 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: C 281 GLU cc_start: 0.8559 (pt0) cc_final: 0.8152 (pm20) REVERT: C 505 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: C 554 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: C 561 PRO cc_start: 0.8476 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: C 661 GLU cc_start: 0.7966 (pm20) cc_final: 0.7520 (pm20) REVERT: C 748 GLU cc_start: 0.8599 (tp30) cc_final: 0.8258 (tp30) outliers start: 62 outliers final: 38 residues processed: 217 average time/residue: 0.4628 time to fit residues: 119.2649 Evaluate side-chains 211 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2203 > 50: distance: 9 - 18: 5.080 distance: 18 - 19: 8.353 distance: 19 - 20: 19.929 distance: 19 - 22: 14.106 distance: 20 - 21: 19.496 distance: 20 - 28: 9.267 distance: 22 - 23: 5.846 distance: 23 - 24: 20.845 distance: 23 - 25: 30.646 distance: 24 - 26: 16.515 distance: 25 - 27: 10.412 distance: 26 - 27: 19.965 distance: 28 - 29: 8.435 distance: 29 - 30: 7.382 distance: 29 - 32: 16.763 distance: 30 - 31: 6.864 distance: 30 - 33: 13.992 distance: 33 - 34: 7.232 distance: 34 - 35: 7.639 distance: 34 - 37: 4.420 distance: 35 - 36: 4.615 distance: 35 - 41: 3.858 distance: 37 - 38: 18.170 distance: 37 - 39: 13.868 distance: 38 - 40: 6.923 distance: 41 - 42: 12.370 distance: 42 - 43: 5.492 distance: 42 - 45: 5.230 distance: 43 - 44: 6.360 distance: 47 - 49: 3.297 distance: 48 - 50: 3.103 distance: 51 - 52: 11.082 distance: 52 - 53: 25.516 distance: 52 - 55: 23.730 distance: 53 - 54: 32.909 distance: 53 - 59: 34.658 distance: 55 - 56: 16.038 distance: 56 - 57: 12.459 distance: 56 - 58: 28.473 distance: 59 - 60: 19.473 distance: 60 - 61: 14.779 distance: 60 - 63: 52.185 distance: 61 - 62: 16.352 distance: 61 - 67: 5.945 distance: 63 - 64: 29.292 distance: 64 - 65: 20.568 distance: 64 - 66: 21.532 distance: 67 - 68: 43.248 distance: 67 - 73: 33.106 distance: 68 - 69: 38.309 distance: 68 - 71: 10.152 distance: 69 - 70: 8.584 distance: 69 - 74: 10.625 distance: 71 - 72: 34.420 distance: 72 - 73: 33.723 distance: 74 - 75: 29.996 distance: 75 - 76: 21.458 distance: 75 - 78: 15.573 distance: 76 - 77: 51.027 distance: 76 - 81: 5.312 distance: 78 - 79: 17.353 distance: 78 - 80: 32.156 distance: 81 - 82: 5.900 distance: 81 - 127: 21.718 distance: 82 - 83: 32.806 distance: 82 - 85: 21.242 distance: 83 - 84: 8.250 distance: 83 - 89: 21.844 distance: 84 - 124: 28.027 distance: 85 - 86: 15.122 distance: 86 - 87: 14.588 distance: 86 - 88: 24.263 distance: 89 - 90: 3.809 distance: 89 - 95: 4.639 distance: 90 - 93: 8.213 distance: 91 - 96: 27.256 distance: 94 - 95: 12.086