Starting phenix.real_space_refine on Mon Jul 6 03:26:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upl_26669/07_2026/7upl_26669.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.075 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 141 5.16 5 C 20472 2.51 5 N 5252 2.21 5 O 6280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32145 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8224 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 57, 'TRANS': 992} Chain breaks: 5 Chain: "B" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8249 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 57, 'TRANS': 995} Chain breaks: 5 Chain: "C" Number of atoms: 8224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8224 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 57, 'TRANS': 992} Chain breaks: 5 Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "F" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} 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 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 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 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 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 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "a" 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 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 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 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 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 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 chiralities: 8 Chain: "C" 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 chiralities: 10 Time building chain proxies: 6.86, per 1000 atoms: 0.21 Number of scatterers: 32145 At special positions: 0 Unit cell: (150.7, 133.1, 242, 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 141 16.00 O 6280 8.00 N 5252 7.00 C 20472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 657 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN C 801 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 282 " " NAG M 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG h 1 " - " ASN C 234 " " NAG o 1 " - " ASN C 717 " " NAG q 1 " - " ASN C1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7546 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 60 sheets defined 21.7% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.628A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.836A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.674A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.789A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.740A pdb=" N ILE A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.818A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.644A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.650A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.306A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.529A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.969A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 853' Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.617A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.882A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.063A pdb=" N TYR A 917 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.846A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.631A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.871A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.933A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.594A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.758A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.785A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 637 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.911A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 783 removed outlier: 4.402A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.752A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 833 removed outlier: 3.718A pdb=" N GLY B 832 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 833 " --> pdb=" O ASP B 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 829 through 833' Processing helix chain 'B' and resid 835 through 841 removed outlier: 3.993A pdb=" N LEU B 841 " --> pdb=" O TYR B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.777A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.870A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.695A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.981A pdb=" N TYR B 917 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 removed outlier: 3.677A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.517A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.390A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (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 984 removed outlier: 4.269A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 4.482A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.773A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.103A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.674A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.730A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.265A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.269A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.838A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 842 removed outlier: 3.527A pdb=" N GLY C 842 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.906A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.794A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 932 removed outlier: 3.827A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 removed outlier: 4.302A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 956 removed outlier: 4.352A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 966 removed outlier: 3.698A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.290A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.722A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.573A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.633A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 188' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.997A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 213 through 215 No H-bonds generated for 'chain 'I' and resid 213 through 215' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.995A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.911A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.305A 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: 3.542A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.884A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.753A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.676A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.507A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.992A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.884A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.725A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.436A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.193A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.662A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.705A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.629A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.825A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.598A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.789A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 6.495A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.762A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.027A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.596A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.883A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.977A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.963A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.963A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.990A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.003A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN D 139 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 175 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR D 179 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 146 through 151 Processing sheet with id=AF1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.795A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'E' and resid 127 through 130 removed outlier: 4.911A pdb=" N ALA E 143 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL E 190 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY E 145 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL E 188 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU E 147 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER E 186 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS E 149 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU E 184 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER E 183 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA E 174 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER E 185 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE E 172 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 187 " --> pdb=" O HIS E 170 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 156 through 160 removed outlier: 4.600A pdb=" N TYR E 200 " --> pdb=" O VAL E 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.781A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.765A pdb=" N ARG F 59 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE F 50 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG F 98 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR F 108 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 127 through 130 removed outlier: 4.077A pdb=" N ASP F 150 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR F 182 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 181 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU F 176 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER F 183 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA F 174 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER F 185 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 157 through 159 Processing sheet with id=AG2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AG4, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.895A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 115 through 119 removed outlier: 3.932A pdb=" N VAL I 134 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU I 180 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 145 through 151 1089 hydrogen bonds defined for protein. 2847 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: 8.19 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10175 1.35 - 1.47: 8311 1.47 - 1.59: 14226 1.59 - 1.72: 0 1.72 - 1.84: 175 Bond restraints: 32887 Sorted by residual: bond pdb=" C GLU B 214 " pdb=" N PRO B 214A" ideal model delta sigma weight residual 1.335 1.361 -0.026 8.70e-03 1.32e+04 8.77e+00 bond pdb=" C7 NAG G 1 " pdb=" O7 NAG G 1 " ideal model delta sigma weight residual 1.222 1.278 -0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" C1 NAG q 2 " pdb=" O5 NAG q 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 32882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 43817 2.06 - 4.12: 841 4.12 - 6.18: 82 6.18 - 8.25: 13 8.25 - 10.31: 4 Bond angle restraints: 44757 Sorted by residual: angle pdb=" C THR A1100 " pdb=" N HIS A1101 " pdb=" CA HIS A1101 " ideal model delta sigma weight residual 122.87 113.06 9.81 1.61e+00 3.86e-01 3.71e+01 angle pdb=" N GLY A 311 " pdb=" CA GLY A 311 " pdb=" C GLY A 311 " ideal model delta sigma weight residual 110.20 116.78 -6.58 1.32e+00 5.74e-01 2.48e+01 angle pdb=" N PRO B 214A" pdb=" CA PRO B 214A" pdb=" C PRO B 214A" ideal model delta sigma weight residual 110.21 116.26 -6.05 1.64e+00 3.72e-01 1.36e+01 angle pdb=" C SER E 209 " pdb=" N ASN E 210 " pdb=" CA ASN E 210 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C SER D 30 " pdb=" N ASN D 31 " pdb=" CA ASN D 31 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.76e+00 ... (remaining 44752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17540 17.99 - 35.98: 1368 35.98 - 53.96: 227 53.96 - 71.95: 46 71.95 - 89.94: 43 Dihedral angle restraints: 19224 sinusoidal: 7484 harmonic: 11740 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 5.24 87.76 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 5.48 87.52 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 175.90 -82.90 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 19221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4527 0.076 - 0.152: 679 0.152 - 0.228: 11 0.228 - 0.305: 7 0.305 - 0.381: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 5222 not shown) Planarity restraints: 5735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 97 " -0.030 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" CG TRP I 97 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP I 97 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP I 97 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP I 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 97 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 97 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 97 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 97 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 152 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO F 153 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 153 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 153 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 214 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO B 214A" 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 214A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 214A" -0.043 5.00e-02 4.00e+02 ... (remaining 5732 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 431 2.65 - 3.21: 29646 3.21 - 3.77: 43898 3.77 - 4.34: 57381 4.34 - 4.90: 95231 Nonbonded interactions: 226587 Sorted by model distance: nonbonded pdb=" OG SER F 159 " pdb=" OD1 ASN F 203 " model vdw 2.086 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" OE1 GLU A 516 " model vdw 2.091 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 22 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR D 165 " pdb=" OG SER D 175 " model vdw 2.119 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.170 3.040 ... (remaining 226582 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 1308) selection = (chain 'B' and (resid 27 through 678 or resid 689 through 1308)) selection = (chain 'C' and resid 27 through 1308) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'o' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.770 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32990 Z= 0.196 Angle : 0.703 10.727 45015 Z= 0.362 Chirality : 0.049 0.381 5225 Planarity : 0.005 0.082 5694 Dihedral : 13.641 89.941 11534 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 3987 helix: -0.68 (0.19), residues: 707 sheet: 0.13 (0.16), residues: 1013 loop : -1.40 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1107 TYR 0.043 0.002 TYR C 873 PHE 0.030 0.002 PHE B 906 TRP 0.059 0.002 TRP I 97 HIS 0.009 0.001 HIS F 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (32887) covalent geometry : angle 0.68090 / 0.36 (44757) SS BOND : bond 0.00521 / 0.33 ( 48) SS BOND : angle 1.60083 / 1.14 ( 96) hydrogen bonds : bond 0.15105 / 9.71 ( 1069) hydrogen bonds : angle 6.64653 / 4.66 ( 2847) Misc. bond : bond 0.02007 / 1.06 ( 1) link_BETA1-4 : bond 0.00730 / 0.48 ( 13) link_BETA1-4 : angle 3.89982 / 2.64 ( 39) link_NAG-ASN : bond 0.00562 / 0.29 ( 41) link_NAG-ASN : angle 2.34652 / 1.42 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8503 (p90) cc_final: 0.8263 (p90) REVERT: A 634 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.7129 (tpt90) REVERT: A 985 ASP cc_start: 0.7126 (t0) cc_final: 0.6444 (m-30) REVERT: B 191 GLU cc_start: 0.8028 (tt0) cc_final: 0.7715 (mm-30) REVERT: B 428 ASP cc_start: 0.8828 (m-30) cc_final: 0.8594 (p0) REVERT: B 516 GLU cc_start: 0.8026 (tp30) cc_final: 0.7810 (tp30) REVERT: B 564 GLN cc_start: 0.8178 (tp40) cc_final: 0.7406 (tp40) REVERT: B 572 THR cc_start: 0.8604 (m) cc_final: 0.8138 (p) REVERT: B 578 ASP cc_start: 0.8144 (t0) cc_final: 0.7777 (t0) REVERT: C 568 ASP cc_start: 0.7360 (t0) cc_final: 0.6572 (p0) REVERT: C 968 SER cc_start: 0.9494 (m) cc_final: 0.9279 (p) REVERT: F 111 GLN cc_start: 0.6612 (pm20) cc_final: 0.6036 (pm20) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2084 time to fit residues: 102.4319 Evaluate side-chains 132 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 207 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN A 907 ASN A1142 GLN B 99 ASN B 343 ASN B 542 ASN B 957 GLN B1101 HIS C 207 HIS C 334 ASN C 370 ASN C 853 GLN C 992 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.127048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085448 restraints weight = 93282.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084235 restraints weight = 74161.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084483 restraints weight = 66617.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084605 restraints weight = 69595.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084506 restraints weight = 61640.964| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32990 Z= 0.149 Angle : 0.648 14.748 45015 Z= 0.330 Chirality : 0.047 0.320 5225 Planarity : 0.005 0.064 5694 Dihedral : 5.039 29.406 4319 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 3987 helix: -0.30 (0.19), residues: 730 sheet: 0.09 (0.16), residues: 1012 loop : -1.44 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 38 TYR 0.030 0.001 TYR C 873 PHE 0.023 0.001 PHE A 823 TRP 0.020 0.002 TRP I 97 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (32887) covalent geometry : angle 0.62879 / 0.33 (44757) SS BOND : bond 0.00482 / 0.29 ( 48) SS BOND : angle 1.49471 / 1.05 ( 96) hydrogen bonds : bond 0.05927 / 3.77 ( 1069) hydrogen bonds : angle 5.47651 / 3.85 ( 2847) Misc. bond : bond 0.01011 / 0.53 ( 1) link_BETA1-4 : bond 0.00693 / 0.47 ( 13) link_BETA1-4 : angle 2.99297 / 2.03 ( 39) link_NAG-ASN : bond 0.00480 / 0.26 ( 41) link_NAG-ASN : angle 2.26833 / 1.42 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8464 (p90) cc_final: 0.8150 (p90) REVERT: A 634 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7143 (tpt90) REVERT: B 564 GLN cc_start: 0.8099 (tp40) cc_final: 0.7621 (tp40) REVERT: B 572 THR cc_start: 0.8486 (m) cc_final: 0.8257 (p) REVERT: C 568 ASP cc_start: 0.7085 (t0) cc_final: 0.6501 (p0) REVERT: F 38 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7223 (ttp80) REVERT: F 48 MET cc_start: 0.7609 (mtt) cc_final: 0.6739 (tpp) REVERT: I 23 CYS cc_start: 0.4417 (p) cc_final: 0.3323 (p) REVERT: I 46 LEU cc_start: 0.8934 (tp) cc_final: 0.8730 (tp) outliers start: 4 outliers final: 1 residues processed: 194 average time/residue: 0.1933 time to fit residues: 63.7380 Evaluate side-chains 131 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 219 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.0050 chunk 74 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 380 optimal weight: 6.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN C 625 HIS C 953 ASN C 965 GLN I 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.129104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096768 restraints weight = 91996.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095030 restraints weight = 125519.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096478 restraints weight = 102589.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097213 restraints weight = 67239.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097569 restraints weight = 66810.474| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32990 Z= 0.112 Angle : 0.597 16.202 45015 Z= 0.300 Chirality : 0.046 0.412 5225 Planarity : 0.004 0.061 5694 Dihedral : 4.761 26.951 4319 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3987 helix: -0.05 (0.20), residues: 734 sheet: 0.12 (0.16), residues: 1000 loop : -1.34 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.023 0.001 TYR A 453 PHE 0.018 0.001 PHE F 152 TRP 0.014 0.001 TRP D 97 HIS 0.009 0.001 HIS I 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (32887) covalent geometry : angle 0.57657 / 0.30 (44757) SS BOND : bond 0.00457 / 0.27 ( 48) SS BOND : angle 1.54105 / 1.06 ( 96) hydrogen bonds : bond 0.04964 / 3.15 ( 1069) hydrogen bonds : angle 5.11076 / 3.59 ( 2847) Misc. bond : bond 0.01102 / 0.58 ( 1) link_BETA1-4 : bond 0.00751 / 0.48 ( 13) link_BETA1-4 : angle 2.92494 / 1.96 ( 39) link_NAG-ASN : bond 0.00451 / 0.26 ( 41) link_NAG-ASN : angle 2.17731 / 1.37 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8226 (p90) cc_final: 0.8001 (p90) REVERT: B 101 ILE cc_start: 0.8016 (pt) cc_final: 0.7526 (pt) REVERT: B 368 LEU cc_start: 0.8985 (mp) cc_final: 0.8696 (mp) REVERT: B 564 GLN cc_start: 0.7940 (tp40) cc_final: 0.7662 (tp40) REVERT: B 572 THR cc_start: 0.8689 (m) cc_final: 0.8426 (p) REVERT: C 884 SER cc_start: 0.8899 (m) cc_final: 0.8612 (t) REVERT: E 93 MET cc_start: 0.6096 (ttt) cc_final: 0.5605 (ttp) REVERT: F 38 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7889 (ttp80) REVERT: F 48 MET cc_start: 0.7881 (mtt) cc_final: 0.7190 (tpp) REVERT: F 59 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7220 (mpp80) REVERT: F 93 MET cc_start: 0.7126 (tpt) cc_final: 0.6691 (mmm) REVERT: I 62 PHE cc_start: 0.6423 (m-80) cc_final: 0.5469 (m-80) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.1988 time to fit residues: 70.5610 Evaluate side-chains 130 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 214 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 351 optimal weight: 30.0000 chunk 258 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 369 optimal weight: 30.0000 chunk 360 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS D 125 GLN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.096116 restraints weight = 92213.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093859 restraints weight = 132655.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095350 restraints weight = 112217.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096222 restraints weight = 71579.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096392 restraints weight = 68437.480| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32990 Z= 0.141 Angle : 0.609 17.636 45015 Z= 0.308 Chirality : 0.046 0.418 5225 Planarity : 0.005 0.139 5694 Dihedral : 4.769 24.769 4319 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3987 helix: 0.00 (0.20), residues: 731 sheet: 0.14 (0.16), residues: 1011 loop : -1.34 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 983 TYR 0.023 0.001 TYR C 873 PHE 0.032 0.001 PHE A 823 TRP 0.029 0.001 TRP D 97 HIS 0.011 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (32887) covalent geometry : angle 0.58908 / 0.30 (44757) SS BOND : bond 0.00463 / 0.28 ( 48) SS BOND : angle 1.62681 / 1.18 ( 96) hydrogen bonds : bond 0.05220 / 3.33 ( 1069) hydrogen bonds : angle 5.09657 / 3.57 ( 2847) Misc. bond : bond 0.01189 / 0.63 ( 1) link_BETA1-4 : bond 0.00731 / 0.52 ( 13) link_BETA1-4 : angle 2.90555 / 1.98 ( 39) link_NAG-ASN : bond 0.00493 / 0.26 ( 41) link_NAG-ASN : angle 2.15161 / 1.35 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8292 (p90) cc_final: 0.8092 (p90) REVERT: A 634 ARG cc_start: 0.7813 (tmt-80) cc_final: 0.7457 (tpt90) REVERT: B 516 GLU cc_start: 0.7717 (tp30) cc_final: 0.7475 (tp30) REVERT: B 564 GLN cc_start: 0.7996 (tp40) cc_final: 0.7698 (tp40) REVERT: B 572 THR cc_start: 0.8715 (m) cc_final: 0.8456 (p) REVERT: B 869 MET cc_start: 0.8292 (mpp) cc_final: 0.8073 (mpp) REVERT: C 884 SER cc_start: 0.9012 (m) cc_final: 0.8623 (t) REVERT: E 93 MET cc_start: 0.6113 (ttt) cc_final: 0.5843 (ttp) REVERT: F 28 ASN cc_start: 0.8037 (m110) cc_final: 0.7492 (t0) REVERT: F 38 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8102 (ttp80) REVERT: F 48 MET cc_start: 0.7885 (mtt) cc_final: 0.7280 (tpp) REVERT: F 59 ARG cc_start: 0.7483 (mtt-85) cc_final: 0.6968 (mtm-85) REVERT: F 93 MET cc_start: 0.7103 (tpt) cc_final: 0.6675 (mmm) REVERT: I 36 TYR cc_start: 0.7937 (m-80) cc_final: 0.7444 (m-80) REVERT: I 62 PHE cc_start: 0.6407 (m-80) cc_final: 0.5459 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1937 time to fit residues: 61.8786 Evaluate side-chains 121 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 157 optimal weight: 0.8980 chunk 262 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 201 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 395 optimal weight: 30.0000 chunk 313 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS D 37 GLN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.129129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084540 restraints weight = 92931.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086342 restraints weight = 76448.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086825 restraints weight = 55340.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086768 restraints weight = 51177.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086962 restraints weight = 51956.706| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32990 Z= 0.112 Angle : 0.585 17.322 45015 Z= 0.293 Chirality : 0.046 0.430 5225 Planarity : 0.004 0.068 5694 Dihedral : 4.636 25.767 4319 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 3987 helix: 0.11 (0.20), residues: 733 sheet: 0.21 (0.16), residues: 1005 loop : -1.34 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.028 0.001 TYR A 501 PHE 0.021 0.001 PHE A 888 TRP 0.045 0.001 TRP D 97 HIS 0.013 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (32887) covalent geometry : angle 0.56648 / 0.29 (44757) SS BOND : bond 0.00412 / 0.26 ( 48) SS BOND : angle 1.35296 / 0.94 ( 96) hydrogen bonds : bond 0.04740 / 3.02 ( 1069) hydrogen bonds : angle 4.94997 / 3.48 ( 2847) Misc. bond : bond 0.01163 / 0.61 ( 1) link_BETA1-4 : bond 0.00753 / 0.53 ( 13) link_BETA1-4 : angle 2.87883 / 1.94 ( 39) link_NAG-ASN : bond 0.00441 / 0.24 ( 41) link_NAG-ASN : angle 2.06646 / 1.28 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8364 (p90) cc_final: 0.8090 (p90) REVERT: A 634 ARG cc_start: 0.7957 (tmt-80) cc_final: 0.7602 (tpt90) REVERT: B 452 LEU cc_start: 0.8472 (mt) cc_final: 0.8217 (mt) REVERT: B 516 GLU cc_start: 0.7831 (tp30) cc_final: 0.7507 (tp30) REVERT: B 564 GLN cc_start: 0.8094 (tp40) cc_final: 0.7628 (tp40) REVERT: B 572 THR cc_start: 0.8556 (m) cc_final: 0.8238 (p) REVERT: C 884 SER cc_start: 0.9045 (m) cc_final: 0.8793 (t) REVERT: D 86 TYR cc_start: 0.8699 (m-80) cc_final: 0.8173 (m-80) REVERT: E 93 MET cc_start: 0.6285 (ttt) cc_final: 0.6033 (ttp) REVERT: F 38 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8197 (ttp80) REVERT: F 48 MET cc_start: 0.7862 (mtt) cc_final: 0.7339 (mtp) REVERT: F 59 ARG cc_start: 0.7568 (mtt-85) cc_final: 0.6859 (mtm-85) REVERT: F 93 MET cc_start: 0.7318 (tpt) cc_final: 0.7009 (mmm) REVERT: F 100 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7723 (tm-30) REVERT: I 23 CYS cc_start: 0.4194 (p) cc_final: 0.3534 (p) REVERT: I 36 TYR cc_start: 0.8149 (m-80) cc_final: 0.7524 (m-80) REVERT: I 62 PHE cc_start: 0.6762 (m-80) cc_final: 0.6044 (m-80) REVERT: I 83 ILE cc_start: 0.6820 (mp) cc_final: 0.6440 (mp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1851 time to fit residues: 58.7613 Evaluate side-chains 121 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 179 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 304 optimal weight: 0.0470 chunk 266 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 354 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN A1101 HIS C 953 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.128596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.086053 restraints weight = 92772.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085944 restraints weight = 69378.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085786 restraints weight = 57179.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086159 restraints weight = 60786.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086158 restraints weight = 54658.034| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32990 Z= 0.126 Angle : 0.592 17.522 45015 Z= 0.297 Chirality : 0.046 0.408 5225 Planarity : 0.004 0.070 5694 Dihedral : 4.619 24.794 4319 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 3987 helix: 0.14 (0.20), residues: 730 sheet: 0.12 (0.16), residues: 1025 loop : -1.30 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.019 0.001 TYR C 873 PHE 0.035 0.001 PHE A 823 TRP 0.034 0.001 TRP D 97 HIS 0.011 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (32887) covalent geometry : angle 0.57418 / 0.29 (44757) SS BOND : bond 0.00415 / 0.26 ( 48) SS BOND : angle 1.38823 / 0.98 ( 96) hydrogen bonds : bond 0.04907 / 3.13 ( 1069) hydrogen bonds : angle 4.95115 / 3.47 ( 2847) Misc. bond : bond 0.01210 / 0.64 ( 1) link_BETA1-4 : bond 0.00836 / 0.54 ( 13) link_BETA1-4 : angle 2.89027 / 1.96 ( 39) link_NAG-ASN : bond 0.00423 / 0.23 ( 41) link_NAG-ASN : angle 2.04673 / 1.28 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8408 (p90) cc_final: 0.8155 (p90) REVERT: A 634 ARG cc_start: 0.7884 (tmt-80) cc_final: 0.7585 (tpt90) REVERT: B 516 GLU cc_start: 0.7826 (tp30) cc_final: 0.7484 (tp30) REVERT: B 564 GLN cc_start: 0.8095 (tp40) cc_final: 0.7642 (tp40) REVERT: B 572 THR cc_start: 0.8571 (m) cc_final: 0.8258 (p) REVERT: C 884 SER cc_start: 0.9105 (m) cc_final: 0.8797 (t) REVERT: D 86 TYR cc_start: 0.8752 (m-80) cc_final: 0.8215 (m-80) REVERT: F 38 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8082 (ttp80) REVERT: F 48 MET cc_start: 0.7895 (mtt) cc_final: 0.7187 (mtp) REVERT: F 93 MET cc_start: 0.7393 (tpt) cc_final: 0.6912 (mmm) REVERT: F 100 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7743 (tm-30) REVERT: I 23 CYS cc_start: 0.4400 (p) cc_final: 0.3730 (p) REVERT: I 36 TYR cc_start: 0.8114 (m-80) cc_final: 0.7536 (m-80) REVERT: I 62 PHE cc_start: 0.6754 (m-80) cc_final: 0.6190 (m-80) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1886 time to fit residues: 56.1974 Evaluate side-chains 117 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 264 optimal weight: 0.0570 chunk 383 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 387 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS I 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084836 restraints weight = 93244.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086612 restraints weight = 74100.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086847 restraints weight = 54342.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086991 restraints weight = 52078.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.087216 restraints weight = 52012.302| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 32990 Z= 0.106 Angle : 0.576 17.217 45015 Z= 0.287 Chirality : 0.046 0.411 5225 Planarity : 0.004 0.074 5694 Dihedral : 4.506 23.638 4319 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3987 helix: 0.26 (0.20), residues: 730 sheet: 0.17 (0.16), residues: 1029 loop : -1.26 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 143 TYR 0.022 0.001 TYR D 91 PHE 0.018 0.001 PHE A 888 TRP 0.020 0.001 TRP D 97 HIS 0.012 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (32887) covalent geometry : angle 0.55798 / 0.28 (44757) SS BOND : bond 0.00368 / 0.23 ( 48) SS BOND : angle 1.27853 / 0.89 ( 96) hydrogen bonds : bond 0.04509 / 2.87 ( 1069) hydrogen bonds : angle 4.82187 / 3.38 ( 2847) Misc. bond : bond 0.01201 / 0.63 ( 1) link_BETA1-4 : bond 0.00742 / 0.51 ( 13) link_BETA1-4 : angle 2.83444 / 1.91 ( 39) link_NAG-ASN : bond 0.00548 / 0.26 ( 41) link_NAG-ASN : angle 2.06100 / 1.29 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8117 (p0) cc_final: 0.7837 (p0) REVERT: A 265 TYR cc_start: 0.8380 (p90) cc_final: 0.8140 (p90) REVERT: A 634 ARG cc_start: 0.7893 (tmt-80) cc_final: 0.7593 (tpt90) REVERT: B 516 GLU cc_start: 0.7755 (tp30) cc_final: 0.7427 (tp30) REVERT: B 564 GLN cc_start: 0.8093 (tp40) cc_final: 0.7630 (tp40) REVERT: B 572 THR cc_start: 0.8543 (m) cc_final: 0.8249 (p) REVERT: C 884 SER cc_start: 0.9023 (m) cc_final: 0.8752 (t) REVERT: D 86 TYR cc_start: 0.8690 (m-80) cc_final: 0.8105 (m-80) REVERT: E 93 MET cc_start: 0.6332 (ttt) cc_final: 0.5825 (tpt) REVERT: F 28 ASN cc_start: 0.7818 (m110) cc_final: 0.7132 (t0) REVERT: F 38 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8190 (ttp80) REVERT: F 48 MET cc_start: 0.7920 (mtt) cc_final: 0.7391 (mtp) REVERT: F 100 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7754 (tm-30) REVERT: I 23 CYS cc_start: 0.4006 (p) cc_final: 0.3511 (p) REVERT: I 36 TYR cc_start: 0.8116 (m-80) cc_final: 0.7531 (m-80) REVERT: I 62 PHE cc_start: 0.6748 (m-80) cc_final: 0.6158 (m-80) REVERT: I 124 GLU cc_start: 0.7335 (tt0) cc_final: 0.6925 (mp0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1796 time to fit residues: 56.7195 Evaluate side-chains 113 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 138 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 111 optimal weight: 0.0870 chunk 368 optimal weight: 0.0170 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 323 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS A1106 GLN B 505 HIS ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.130393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097476 restraints weight = 92724.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096271 restraints weight = 107009.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097177 restraints weight = 94587.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098166 restraints weight = 61252.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098592 restraints weight = 56609.574| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32990 Z= 0.100 Angle : 0.563 16.952 45015 Z= 0.280 Chirality : 0.046 0.388 5225 Planarity : 0.004 0.071 5694 Dihedral : 4.349 22.299 4319 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 3987 helix: 0.40 (0.20), residues: 727 sheet: 0.26 (0.16), residues: 1025 loop : -1.20 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 143 TYR 0.017 0.001 TYR D 91 PHE 0.027 0.001 PHE A 823 TRP 0.013 0.001 TRP D 97 HIS 0.009 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (32887) covalent geometry : angle 0.54604 / 0.28 (44757) SS BOND : bond 0.00359 / 0.24 ( 48) SS BOND : angle 1.28664 / 0.89 ( 96) hydrogen bonds : bond 0.04102 / 2.61 ( 1069) hydrogen bonds : angle 4.70053 / 3.29 ( 2847) Misc. bond : bond 0.01190 / 0.63 ( 1) link_BETA1-4 : bond 0.00719 / 0.49 ( 13) link_BETA1-4 : angle 2.74689 / 1.85 ( 39) link_NAG-ASN : bond 0.00490 / 0.27 ( 41) link_NAG-ASN : angle 1.99845 / 1.23 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7799 (p0) cc_final: 0.7496 (p0) REVERT: A 191 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7574 (mt-10) REVERT: A 233 ILE cc_start: 0.7873 (tp) cc_final: 0.7502 (mm) REVERT: A 634 ARG cc_start: 0.7735 (tmt-80) cc_final: 0.7514 (tpt90) REVERT: B 516 GLU cc_start: 0.7589 (tp30) cc_final: 0.7329 (tp30) REVERT: B 564 GLN cc_start: 0.8018 (tp40) cc_final: 0.7672 (tp40) REVERT: C 884 SER cc_start: 0.8832 (m) cc_final: 0.8589 (t) REVERT: D 86 TYR cc_start: 0.8155 (m-80) cc_final: 0.7592 (m-80) REVERT: E 93 MET cc_start: 0.6132 (ttt) cc_final: 0.5685 (tpt) REVERT: F 28 ASN cc_start: 0.7721 (m110) cc_final: 0.7219 (t0) REVERT: F 38 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8571 (ttp80) REVERT: I 36 TYR cc_start: 0.7785 (m-80) cc_final: 0.7408 (m-80) REVERT: I 62 PHE cc_start: 0.6537 (m-80) cc_final: 0.5776 (m-80) REVERT: I 124 GLU cc_start: 0.7439 (tt0) cc_final: 0.6938 (mp0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1854 time to fit residues: 59.6119 Evaluate side-chains 114 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 326 optimal weight: 0.2980 chunk 299 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 200 optimal weight: 0.0770 chunk 349 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS C 955 ASN C1011 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.087883 restraints weight = 92394.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087976 restraints weight = 70665.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088043 restraints weight = 57785.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088355 restraints weight = 58399.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.088546 restraints weight = 51828.780| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32990 Z= 0.104 Angle : 0.565 17.073 45015 Z= 0.281 Chirality : 0.045 0.389 5225 Planarity : 0.004 0.074 5694 Dihedral : 4.320 21.723 4319 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 3987 helix: 0.48 (0.20), residues: 721 sheet: 0.27 (0.16), residues: 1025 loop : -1.19 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 38 TYR 0.018 0.001 TYR D 91 PHE 0.018 0.001 PHE B 906 TRP 0.019 0.001 TRP F 36 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (32887) covalent geometry : angle 0.54834 / 0.28 (44757) SS BOND : bond 0.00394 / 0.26 ( 48) SS BOND : angle 1.30582 / 0.91 ( 96) hydrogen bonds : bond 0.04201 / 2.68 ( 1069) hydrogen bonds : angle 4.68245 / 3.27 ( 2847) Misc. bond : bond 0.01175 / 0.62 ( 1) link_BETA1-4 : bond 0.00720 / 0.50 ( 13) link_BETA1-4 : angle 2.71345 / 1.83 ( 39) link_NAG-ASN : bond 0.00452 / 0.24 ( 41) link_NAG-ASN : angle 1.97333 / 1.22 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8105 (p0) cc_final: 0.7818 (p0) REVERT: A 233 ILE cc_start: 0.7948 (tp) cc_final: 0.7585 (mm) REVERT: A 634 ARG cc_start: 0.7866 (tmt-80) cc_final: 0.7531 (tpt90) REVERT: B 516 GLU cc_start: 0.7760 (tp30) cc_final: 0.7422 (tp30) REVERT: B 564 GLN cc_start: 0.8098 (tp40) cc_final: 0.7644 (tp40) REVERT: B 1029 MET cc_start: 0.8832 (tpp) cc_final: 0.8374 (tmm) REVERT: C 884 SER cc_start: 0.9051 (m) cc_final: 0.8790 (t) REVERT: D 86 TYR cc_start: 0.8685 (m-80) cc_final: 0.8100 (m-80) REVERT: E 93 MET cc_start: 0.6274 (ttt) cc_final: 0.5743 (tpt) REVERT: F 28 ASN cc_start: 0.7728 (m110) cc_final: 0.7168 (t0) REVERT: F 38 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8102 (ttp80) REVERT: F 100 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7718 (tm-30) REVERT: I 23 CYS cc_start: 0.4062 (p) cc_final: 0.3566 (p) REVERT: I 36 TYR cc_start: 0.8063 (m-80) cc_final: 0.7585 (m-80) REVERT: I 62 PHE cc_start: 0.6774 (m-80) cc_final: 0.6190 (m-80) REVERT: I 124 GLU cc_start: 0.7341 (tt0) cc_final: 0.6881 (mp0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1812 time to fit residues: 56.4846 Evaluate side-chains 110 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 272 optimal weight: 1.9990 chunk 384 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 317 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 393 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS C 762 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.129556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.086366 restraints weight = 93032.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087121 restraints weight = 71667.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087151 restraints weight = 54969.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087047 restraints weight = 59186.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087051 restraints weight = 60728.680| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32990 Z= 0.109 Angle : 0.570 17.090 45015 Z= 0.283 Chirality : 0.046 0.386 5225 Planarity : 0.004 0.076 5694 Dihedral : 4.319 21.476 4319 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 3987 helix: 0.51 (0.21), residues: 713 sheet: 0.34 (0.16), residues: 995 loop : -1.19 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 38 TYR 0.019 0.001 TYR D 91 PHE 0.021 0.001 PHE B 906 TRP 0.012 0.001 TRP F 47 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (32887) covalent geometry : angle 0.55310 / 0.28 (44757) SS BOND : bond 0.00463 / 0.33 ( 48) SS BOND : angle 1.28076 / 0.88 ( 96) hydrogen bonds : bond 0.04296 / 2.75 ( 1069) hydrogen bonds : angle 4.68921 / 3.27 ( 2847) Misc. bond : bond 0.01182 / 0.62 ( 1) link_BETA1-4 : bond 0.00714 / 0.50 ( 13) link_BETA1-4 : angle 2.70608 / 1.83 ( 39) link_NAG-ASN : bond 0.00444 / 0.23 ( 41) link_NAG-ASN : angle 1.96982 / 1.22 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8114 (p0) cc_final: 0.7767 (p0) REVERT: A 233 ILE cc_start: 0.7961 (tp) cc_final: 0.7543 (mm) REVERT: A 634 ARG cc_start: 0.7840 (tmt-80) cc_final: 0.7470 (tpt90) REVERT: B 516 GLU cc_start: 0.7766 (tp30) cc_final: 0.7425 (tp30) REVERT: B 564 GLN cc_start: 0.8128 (tp40) cc_final: 0.7657 (tp40) REVERT: B 869 MET cc_start: 0.8512 (mpp) cc_final: 0.8268 (mpp) REVERT: B 1029 MET cc_start: 0.8845 (tpp) cc_final: 0.8343 (tmm) REVERT: C 884 SER cc_start: 0.9017 (m) cc_final: 0.8707 (t) REVERT: D 86 TYR cc_start: 0.8672 (m-80) cc_final: 0.8073 (m-80) REVERT: E 93 MET cc_start: 0.6284 (ttt) cc_final: 0.5750 (tpt) REVERT: F 28 ASN cc_start: 0.7714 (m110) cc_final: 0.7094 (t0) REVERT: F 38 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8053 (ttp80) REVERT: F 100 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7766 (tm-30) REVERT: I 23 CYS cc_start: 0.3876 (p) cc_final: 0.3495 (p) REVERT: I 36 TYR cc_start: 0.8034 (m-80) cc_final: 0.7625 (m-80) REVERT: I 62 PHE cc_start: 0.6771 (m-80) cc_final: 0.6206 (m-80) REVERT: I 124 GLU cc_start: 0.7357 (tt0) cc_final: 0.6889 (mp0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1912 time to fit residues: 55.3908 Evaluate side-chains 111 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 288 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 270 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 364 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1106 GLN C 641 ASN D 53 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.122335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080589 restraints weight = 91436.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079866 restraints weight = 72902.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079249 restraints weight = 71751.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.079728 restraints weight = 71883.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.079868 restraints weight = 64400.633| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32990 Z= 0.253 Angle : 0.747 18.619 45015 Z= 0.381 Chirality : 0.050 0.430 5225 Planarity : 0.005 0.075 5694 Dihedral : 5.087 24.150 4319 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3987 helix: -0.10 (0.20), residues: 720 sheet: 0.09 (0.16), residues: 1002 loop : -1.42 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 905 TYR 0.035 0.002 TYR C 873 PHE 0.039 0.002 PHE C 906 TRP 0.026 0.002 TRP D 97 HIS 0.012 0.002 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 (32887) covalent geometry : angle 0.72872 / 0.38 (44757) SS BOND : bond 0.00521 / 0.33 ( 48) SS BOND : angle 1.84973 / 1.29 ( 96) hydrogen bonds : bond 0.06840 / 4.42 ( 1069) hydrogen bonds : angle 5.42290 / 3.77 ( 2847) Misc. bond : bond 0.01273 / 0.67 ( 1) link_BETA1-4 : bond 0.00739 / 0.54 ( 13) link_BETA1-4 : angle 3.04322 / 2.11 ( 39) link_NAG-ASN : bond 0.00512 / 0.29 ( 41) link_NAG-ASN : angle 2.27436 / 1.46 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4977.39 seconds wall clock time: 87 minutes 38.75 seconds (5258.75 seconds total)