Starting phenix.real_space_refine on Fri Mar 6 16:07:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upl_26669/03_2026/7upl_26669.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upl_26669/03_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_26669/03_2026/7upl_26669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upl_26669/03_2026/7upl_26669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upl_26669/03_2026/7upl_26669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upl_26669/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.43, per 1000 atoms: 0.23 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: 2.64 Conformation dependent library (CDL) restraints added in 1.3 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: 1.51 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: 7.08 Time building geometry restraints manager: 3.57 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 - 20.45: 18824 20.45 - 40.89: 1249 40.89 - 61.34: 205 61.34 - 81.79: 58 81.79 - 102.24: 22 Dihedral angle restraints: 20358 sinusoidal: 8618 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 20355 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.950 Find NCS groups from input model: 0.950 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 : 14.030 102.237 12668 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 covalent geometry : bond 0.00429 (32887) covalent geometry : angle 0.68090 (44757) SS BOND : bond 0.00521 ( 48) SS BOND : angle 1.60083 ( 96) hydrogen bonds : bond 0.15105 ( 1069) hydrogen bonds : angle 6.64653 ( 2847) Misc. bond : bond 0.02007 ( 1) link_BETA1-4 : bond 0.00730 ( 13) link_BETA1-4 : angle 3.89982 ( 39) link_NAG-ASN : bond 0.00562 ( 41) link_NAG-ASN : angle 2.34652 ( 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 : 1.163 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: 0.1912 time to fit residues: 94.0906 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 : 1.152 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.127063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086558 restraints weight = 93282.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084649 restraints weight = 73724.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084200 restraints weight = 72120.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084840 restraints weight = 76429.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084868 restraints weight = 64692.932| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1259 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= 0.151 Angle : 0.652 14.546 45015 Z= 0.331 Chirality : 0.047 0.311 5225 Planarity : 0.005 0.063 5694 Dihedral : 8.004 79.514 5453 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % 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: -1.21 (0.13), residues: 3987 helix: -0.29 (0.19), residues: 730 sheet: 0.10 (0.16), residues: 1012 loop : -1.44 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 38 TYR 0.030 0.001 TYR C 873 PHE 0.023 0.001 PHE A 823 TRP 0.021 0.001 TRP I 97 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00343 (32887) covalent geometry : angle 0.63175 (44757) SS BOND : bond 0.00520 ( 48) SS BOND : angle 1.48703 ( 96) hydrogen bonds : bond 0.05968 ( 1069) hydrogen bonds : angle 5.47542 ( 2847) Misc. bond : bond 0.01025 ( 1) link_BETA1-4 : bond 0.00647 ( 13) link_BETA1-4 : angle 3.18751 ( 39) link_NAG-ASN : bond 0.00479 ( 41) link_NAG-ASN : angle 2.30619 ( 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 : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8455 (p90) cc_final: 0.8147 (p90) REVERT: A 634 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.7135 (tpt90) REVERT: B 564 GLN cc_start: 0.8090 (tp40) cc_final: 0.7621 (tp40) REVERT: B 572 THR cc_start: 0.8486 (m) cc_final: 0.8255 (p) REVERT: C 568 ASP cc_start: 0.7061 (t0) cc_final: 0.6455 (p0) REVERT: F 38 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7225 (ttp80) REVERT: F 48 MET cc_start: 0.7535 (mtt) cc_final: 0.6723 (tpp) REVERT: I 23 CYS cc_start: 0.4153 (p) cc_final: 0.3166 (p) outliers start: 4 outliers final: 1 residues processed: 194 average time/residue: 0.1781 time to fit residues: 58.6317 Evaluate side-chains 133 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 74 optimal weight: 0.0980 chunk 177 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN C 334 ASN C 625 HIS C 953 ASN C 965 GLN I 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097324 restraints weight = 92071.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097597 restraints weight = 137966.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098250 restraints weight = 103161.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099160 restraints weight = 67737.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099538 restraints weight = 63440.486| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1715 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= 0.115 Angle : 0.601 16.209 45015 Z= 0.301 Chirality : 0.046 0.360 5225 Planarity : 0.004 0.061 5694 Dihedral : 7.375 67.478 5453 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % 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: -1.07 (0.13), residues: 3987 helix: -0.04 (0.20), residues: 734 sheet: 0.11 (0.16), residues: 1002 loop : -1.34 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.022 0.001 TYR C 873 PHE 0.017 0.001 PHE F 152 TRP 0.014 0.001 TRP D 97 HIS 0.005 0.001 HIS I 190 Details of bonding type rmsd covalent geometry : bond 0.00239 (32887) covalent geometry : angle 0.57929 (44757) SS BOND : bond 0.00478 ( 48) SS BOND : angle 1.51789 ( 96) hydrogen bonds : bond 0.04984 ( 1069) hydrogen bonds : angle 5.11094 ( 2847) Misc. bond : bond 0.01138 ( 1) link_BETA1-4 : bond 0.00817 ( 13) link_BETA1-4 : angle 3.12240 ( 39) link_NAG-ASN : bond 0.00581 ( 41) link_NAG-ASN : angle 2.25778 ( 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 : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8223 (p90) cc_final: 0.7993 (p90) REVERT: A 983 ARG cc_start: 0.8335 (ttt180) cc_final: 0.8129 (mmm-85) REVERT: B 101 ILE cc_start: 0.8053 (pt) cc_final: 0.7566 (pt) REVERT: B 368 LEU cc_start: 0.8990 (mp) cc_final: 0.8706 (mp) REVERT: B 564 GLN cc_start: 0.7983 (tp40) cc_final: 0.7652 (tp40) REVERT: B 572 THR cc_start: 0.8730 (m) cc_final: 0.8477 (p) REVERT: C 884 SER cc_start: 0.8949 (m) cc_final: 0.8650 (t) REVERT: E 93 MET cc_start: 0.6052 (ttt) cc_final: 0.5465 (ttp) REVERT: F 38 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7973 (ttp80) REVERT: F 48 MET cc_start: 0.7796 (mtt) cc_final: 0.7057 (tpp) REVERT: F 59 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.7252 (mpp80) REVERT: F 93 MET cc_start: 0.7174 (tpt) cc_final: 0.6809 (mmm) REVERT: I 62 PHE cc_start: 0.6345 (m-80) cc_final: 0.5361 (m-80) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.1862 time to fit residues: 65.8816 Evaluate side-chains 134 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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: 7.9990 chunk 184 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 351 optimal weight: 30.0000 chunk 258 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 369 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B1088 HIS C 953 ASN D 53 ASN D 125 GLN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.125396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082830 restraints weight = 93160.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082273 restraints weight = 71407.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081994 restraints weight = 59959.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082132 restraints weight = 61560.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082221 restraints weight = 60847.932| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32990 Z= 0.215 Angle : 0.701 18.354 45015 Z= 0.357 Chirality : 0.049 0.406 5225 Planarity : 0.005 0.066 5694 Dihedral : 7.421 61.918 5453 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % 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: -1.26 (0.13), residues: 3987 helix: -0.22 (0.20), residues: 723 sheet: -0.03 (0.16), residues: 1015 loop : -1.45 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 98 TYR 0.035 0.002 TYR C 873 PHE 0.040 0.002 PHE B 906 TRP 0.043 0.002 TRP D 97 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00513 (32887) covalent geometry : angle 0.68080 (44757) SS BOND : bond 0.00539 ( 48) SS BOND : angle 1.74147 ( 96) hydrogen bonds : bond 0.06472 ( 1069) hydrogen bonds : angle 5.40328 ( 2847) Misc. bond : bond 0.01203 ( 1) link_BETA1-4 : bond 0.00682 ( 13) link_BETA1-4 : angle 3.18707 ( 39) link_NAG-ASN : bond 0.00543 ( 41) link_NAG-ASN : angle 2.31877 ( 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 175 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 ARG cc_start: 0.8032 (tmt-80) cc_final: 0.7669 (tpt90) REVERT: A 983 ARG cc_start: 0.8414 (ttt180) cc_final: 0.8027 (mmm-85) REVERT: B 516 GLU cc_start: 0.7929 (tp30) cc_final: 0.7647 (tp30) REVERT: B 564 GLN cc_start: 0.8190 (tp40) cc_final: 0.7629 (tp-100) REVERT: C 981 PHE cc_start: 0.7653 (t80) cc_final: 0.7207 (t80) REVERT: E 40 MET cc_start: 0.7345 (tmm) cc_final: 0.7100 (tmm) REVERT: E 48 MET cc_start: 0.7049 (mmt) cc_final: 0.6056 (mtp) REVERT: F 38 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7842 (ttp80) REVERT: F 48 MET cc_start: 0.7786 (mtt) cc_final: 0.7034 (mtp) REVERT: F 93 MET cc_start: 0.7524 (tpt) cc_final: 0.7278 (mmm) REVERT: F 100 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7502 (tm-30) REVERT: I 23 CYS cc_start: 0.4697 (p) cc_final: 0.4049 (p) REVERT: I 36 TYR cc_start: 0.8229 (m-80) cc_final: 0.7637 (m-80) REVERT: I 62 PHE cc_start: 0.6621 (m-80) cc_final: 0.5941 (m-80) outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.1800 time to fit residues: 53.1021 Evaluate side-chains 115 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 1.9990 chunk 262 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 395 optimal weight: 9.9990 chunk 313 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.126511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082024 restraints weight = 93371.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083004 restraints weight = 81341.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083314 restraints weight = 61627.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083441 restraints weight = 55682.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083592 restraints weight = 56684.985| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32990 Z= 0.158 Angle : 0.637 16.309 45015 Z= 0.323 Chirality : 0.047 0.360 5225 Planarity : 0.005 0.066 5694 Dihedral : 7.130 57.554 5453 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -1.23 (0.13), residues: 3987 helix: -0.14 (0.20), residues: 727 sheet: -0.01 (0.16), residues: 1021 loop : -1.46 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 498 TYR 0.025 0.001 TYR A 501 PHE 0.022 0.002 PHE C 906 TRP 0.046 0.001 TRP D 97 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00366 (32887) covalent geometry : angle 0.61709 (44757) SS BOND : bond 0.00492 ( 48) SS BOND : angle 1.50899 ( 96) hydrogen bonds : bond 0.05673 ( 1069) hydrogen bonds : angle 5.22923 ( 2847) Misc. bond : bond 0.01166 ( 1) link_BETA1-4 : bond 0.00836 ( 13) link_BETA1-4 : angle 3.21123 ( 39) link_NAG-ASN : bond 0.00453 ( 41) link_NAG-ASN : angle 2.22972 ( 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 163 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 ARG cc_start: 0.7961 (tmt-80) cc_final: 0.7637 (tpt90) REVERT: A 983 ARG cc_start: 0.8413 (ttt180) cc_final: 0.8015 (mmm-85) REVERT: B 516 GLU cc_start: 0.7919 (tp30) cc_final: 0.7659 (tp30) REVERT: C 981 PHE cc_start: 0.7611 (t80) cc_final: 0.7216 (t80) REVERT: E 48 MET cc_start: 0.7125 (mmt) cc_final: 0.6219 (mtp) REVERT: F 38 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8085 (ttp80) REVERT: F 48 MET cc_start: 0.8000 (mtt) cc_final: 0.7494 (mtp) REVERT: F 93 MET cc_start: 0.7483 (tpt) cc_final: 0.7224 (mmm) REVERT: F 100 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7654 (tm-30) REVERT: I 23 CYS cc_start: 0.4399 (p) cc_final: 0.3781 (p) REVERT: I 36 TYR cc_start: 0.8234 (m-80) cc_final: 0.7687 (m-80) REVERT: I 62 PHE cc_start: 0.6706 (m-80) cc_final: 0.6039 (m-80) REVERT: I 83 ILE cc_start: 0.6805 (mp) cc_final: 0.6405 (mp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1639 time to fit residues: 46.5034 Evaluate side-chains 115 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 0.9990 chunk 218 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN I 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.126265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094752 restraints weight = 92297.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093297 restraints weight = 145361.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094633 restraints weight = 112518.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095760 restraints weight = 73363.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096149 restraints weight = 68425.163| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32990 Z= 0.127 Angle : 0.605 17.096 45015 Z= 0.304 Chirality : 0.046 0.352 5225 Planarity : 0.004 0.070 5694 Dihedral : 6.822 57.062 5453 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: -1.11 (0.13), residues: 3987 helix: 0.01 (0.20), residues: 723 sheet: 0.04 (0.16), residues: 1016 loop : -1.39 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.019 0.001 TYR B 453 PHE 0.020 0.001 PHE B 906 TRP 0.024 0.001 TRP D 97 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00287 (32887) covalent geometry : angle 0.58508 (44757) SS BOND : bond 0.00414 ( 48) SS BOND : angle 1.44097 ( 96) hydrogen bonds : bond 0.05201 ( 1069) hydrogen bonds : angle 5.03237 ( 2847) Misc. bond : bond 0.01236 ( 1) link_BETA1-4 : bond 0.00650 ( 13) link_BETA1-4 : angle 3.11829 ( 39) link_NAG-ASN : bond 0.00509 ( 41) link_NAG-ASN : angle 2.21174 ( 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 166 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 983 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8139 (mmm-85) REVERT: C 884 SER cc_start: 0.9114 (m) cc_final: 0.8708 (t) REVERT: C 981 PHE cc_start: 0.7556 (t80) cc_final: 0.7271 (t80) REVERT: F 38 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8566 (ttp80) REVERT: F 93 MET cc_start: 0.7250 (tpt) cc_final: 0.6969 (mmm) REVERT: I 36 TYR cc_start: 0.7795 (m-80) cc_final: 0.7427 (m-80) REVERT: I 62 PHE cc_start: 0.6595 (m-80) cc_final: 0.5814 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1640 time to fit residues: 46.9740 Evaluate side-chains 109 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 4.9990 chunk 383 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 162 optimal weight: 0.0970 chunk 64 optimal weight: 0.4980 chunk 81 optimal weight: 0.1980 chunk 293 optimal weight: 0.8980 chunk 387 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 197 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 625 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096589 restraints weight = 92397.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093882 restraints weight = 123666.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095353 restraints weight = 106855.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096219 restraints weight = 67505.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096715 restraints weight = 64393.360| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2558 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= 0.106 Angle : 0.585 15.932 45015 Z= 0.291 Chirality : 0.046 0.396 5225 Planarity : 0.004 0.065 5694 Dihedral : 6.469 56.298 5453 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -0.93 (0.13), residues: 3987 helix: 0.13 (0.20), residues: 731 sheet: 0.17 (0.16), residues: 1035 loop : -1.28 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.014 0.001 TYR B 453 PHE 0.022 0.001 PHE C 823 TRP 0.016 0.001 TRP D 97 HIS 0.004 0.001 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00219 (32887) covalent geometry : angle 0.56349 (44757) SS BOND : bond 0.00377 ( 48) SS BOND : angle 1.39474 ( 96) hydrogen bonds : bond 0.04442 ( 1069) hydrogen bonds : angle 4.82512 ( 2847) Misc. bond : bond 0.01170 ( 1) link_BETA1-4 : bond 0.00696 ( 13) link_BETA1-4 : angle 3.01458 ( 39) link_NAG-ASN : bond 0.00507 ( 41) link_NAG-ASN : angle 2.27384 ( 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 169 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7792 (p0) cc_final: 0.7420 (p0) REVERT: A 233 ILE cc_start: 0.7964 (tp) cc_final: 0.7526 (mm) REVERT: A 983 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8139 (mmm-85) REVERT: B 529 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7787 (mmmt) REVERT: B 564 GLN cc_start: 0.8041 (tp40) cc_final: 0.7732 (tp-100) REVERT: C 884 SER cc_start: 0.8944 (m) cc_final: 0.8652 (t) REVERT: C 981 PHE cc_start: 0.7523 (t80) cc_final: 0.7239 (t80) REVERT: E 48 MET cc_start: 0.6580 (mmt) cc_final: 0.5951 (mtp) REVERT: F 28 ASN cc_start: 0.7824 (m110) cc_final: 0.7191 (t0) REVERT: I 36 TYR cc_start: 0.7642 (m-80) cc_final: 0.7331 (m-80) REVERT: I 62 PHE cc_start: 0.6671 (m-80) cc_final: 0.5905 (m-80) REVERT: I 124 GLU cc_start: 0.7472 (tt0) cc_final: 0.7026 (mp0) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1603 time to fit residues: 47.6646 Evaluate side-chains 112 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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: 0.9980 chunk 164 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 368 optimal weight: 0.0570 chunk 104 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 323 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 284 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.128504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096340 restraints weight = 92300.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096948 restraints weight = 124505.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098013 restraints weight = 99045.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.097635 restraints weight = 73761.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097829 restraints weight = 65199.432| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2698 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= 0.102 Angle : 0.576 16.003 45015 Z= 0.286 Chirality : 0.046 0.424 5225 Planarity : 0.004 0.070 5694 Dihedral : 6.223 56.199 5453 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.84 (0.13), residues: 3987 helix: 0.28 (0.20), residues: 726 sheet: 0.20 (0.16), residues: 1013 loop : -1.22 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 38 TYR 0.022 0.001 TYR B 453 PHE 0.015 0.001 PHE F 152 TRP 0.016 0.001 TRP F 47 HIS 0.003 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00218 (32887) covalent geometry : angle 0.55509 (44757) SS BOND : bond 0.00340 ( 48) SS BOND : angle 1.31336 ( 96) hydrogen bonds : bond 0.04264 ( 1069) hydrogen bonds : angle 4.72299 ( 2847) Misc. bond : bond 0.01147 ( 1) link_BETA1-4 : bond 0.00662 ( 13) link_BETA1-4 : angle 2.92736 ( 39) link_NAG-ASN : bond 0.00485 ( 41) link_NAG-ASN : angle 2.32346 ( 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 170 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7719 (p0) cc_final: 0.7343 (p0) REVERT: A 233 ILE cc_start: 0.7913 (tp) cc_final: 0.7458 (mm) REVERT: B 516 GLU cc_start: 0.7667 (tp30) cc_final: 0.7435 (tp30) REVERT: B 529 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7788 (mmmt) REVERT: B 564 GLN cc_start: 0.8020 (tp40) cc_final: 0.7659 (tp-100) REVERT: C 884 SER cc_start: 0.8877 (m) cc_final: 0.8575 (t) REVERT: C 981 PHE cc_start: 0.7581 (t80) cc_final: 0.7302 (t80) REVERT: E 48 MET cc_start: 0.6675 (mmt) cc_final: 0.6220 (mtp) REVERT: F 28 ASN cc_start: 0.7761 (m110) cc_final: 0.7202 (t0) REVERT: F 38 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8191 (ttt-90) REVERT: F 93 MET cc_start: 0.6992 (tpt) cc_final: 0.6606 (tpt) REVERT: I 36 TYR cc_start: 0.7525 (m-80) cc_final: 0.7247 (m-80) REVERT: I 62 PHE cc_start: 0.6568 (m-80) cc_final: 0.5822 (m-80) REVERT: I 124 GLU cc_start: 0.7433 (tt0) cc_final: 0.6956 (mp0) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1666 time to fit residues: 49.6442 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 : 1.154 ------------------------------------------------------------------------------- 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: 20.0000 chunk 299 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 387 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 200 optimal weight: 0.0970 chunk 349 optimal weight: 30.0000 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095420 restraints weight = 92302.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.092734 restraints weight = 132204.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093891 restraints weight = 115436.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095182 restraints weight = 74479.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095283 restraints weight = 66291.560| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2755 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= 0.140 Angle : 0.613 16.336 45015 Z= 0.307 Chirality : 0.046 0.388 5225 Planarity : 0.005 0.125 5694 Dihedral : 6.279 56.315 5453 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.88 (0.13), residues: 3987 helix: 0.20 (0.20), residues: 727 sheet: 0.16 (0.16), residues: 1041 loop : -1.23 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 983 TYR 0.017 0.001 TYR C 873 PHE 0.024 0.001 PHE A 906 TRP 0.018 0.001 TRP D 97 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00324 (32887) covalent geometry : angle 0.59387 (44757) SS BOND : bond 0.00504 ( 48) SS BOND : angle 1.43420 ( 96) hydrogen bonds : bond 0.04962 ( 1069) hydrogen bonds : angle 4.86697 ( 2847) Misc. bond : bond 0.01196 ( 1) link_BETA1-4 : bond 0.00584 ( 13) link_BETA1-4 : angle 2.95389 ( 39) link_NAG-ASN : bond 0.00468 ( 41) link_NAG-ASN : angle 2.24116 ( 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 159 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: B 516 GLU cc_start: 0.7601 (tp30) cc_final: 0.7370 (tp30) REVERT: B 529 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7750 (mmmt) REVERT: B 564 GLN cc_start: 0.8041 (tp40) cc_final: 0.7728 (tp-100) REVERT: C 884 SER cc_start: 0.8922 (m) cc_final: 0.8595 (t) REVERT: C 981 PHE cc_start: 0.7598 (t80) cc_final: 0.7343 (t80) REVERT: E 48 MET cc_start: 0.6727 (mmt) cc_final: 0.6309 (mtp) REVERT: F 28 ASN cc_start: 0.7815 (m110) cc_final: 0.7219 (t0) REVERT: F 93 MET cc_start: 0.6971 (tpt) cc_final: 0.6536 (tpp) REVERT: I 36 TYR cc_start: 0.7649 (m-80) cc_final: 0.7335 (m-80) REVERT: I 62 PHE cc_start: 0.6695 (m-80) cc_final: 0.5967 (m-80) REVERT: I 124 GLU cc_start: 0.7463 (tt0) cc_final: 0.6965 (mp0) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1563 time to fit residues: 43.8995 Evaluate side-chains 108 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 0.2980 chunk 321 optimal weight: 20.0000 chunk 209 optimal weight: 0.5980 chunk 247 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 317 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 393 optimal weight: 30.0000 chunk 133 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS C 641 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082183 restraints weight = 91889.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080607 restraints weight = 73796.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080925 restraints weight = 65999.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081107 restraints weight = 68957.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081173 restraints weight = 62726.915| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32990 Z= 0.184 Angle : 0.665 16.765 45015 Z= 0.337 Chirality : 0.048 0.396 5225 Planarity : 0.005 0.096 5694 Dihedral : 6.592 56.918 5453 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.07 (0.13), residues: 3987 helix: -0.02 (0.20), residues: 722 sheet: 0.11 (0.16), residues: 1012 loop : -1.36 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 983 TYR 0.024 0.001 TYR C 873 PHE 0.025 0.002 PHE B 906 TRP 0.026 0.002 TRP D 97 HIS 0.008 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00436 (32887) covalent geometry : angle 0.64563 (44757) SS BOND : bond 0.00464 ( 48) SS BOND : angle 1.61169 ( 96) hydrogen bonds : bond 0.05931 ( 1069) hydrogen bonds : angle 5.15377 ( 2847) Misc. bond : bond 0.01179 ( 1) link_BETA1-4 : bond 0.00617 ( 13) link_BETA1-4 : angle 3.07090 ( 39) link_NAG-ASN : bond 0.00483 ( 41) link_NAG-ASN : angle 2.28180 ( 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 145 residues out of total 3518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 452 LEU cc_start: 0.8402 (mt) cc_final: 0.8199 (mt) REVERT: B 516 GLU cc_start: 0.7870 (tp30) cc_final: 0.7545 (tp30) REVERT: B 529 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7881 (mmmt) REVERT: B 564 GLN cc_start: 0.8231 (tp40) cc_final: 0.7653 (tp-100) REVERT: C 884 SER cc_start: 0.9368 (m) cc_final: 0.8814 (t) REVERT: C 904 TYR cc_start: 0.8216 (m-10) cc_final: 0.7831 (m-10) REVERT: C 981 PHE cc_start: 0.7797 (t80) cc_final: 0.7357 (t80) REVERT: E 48 MET cc_start: 0.7214 (mmt) cc_final: 0.6360 (mtt) REVERT: F 28 ASN cc_start: 0.7714 (m110) cc_final: 0.7053 (t0) REVERT: F 38 ARG cc_start: 0.7698 (ttp80) cc_final: 0.6824 (ttp80) REVERT: F 93 MET cc_start: 0.7095 (tpt) cc_final: 0.6703 (tpp) REVERT: I 23 CYS cc_start: 0.4562 (p) cc_final: 0.4109 (p) REVERT: I 36 TYR cc_start: 0.8119 (m-80) cc_final: 0.7634 (m-80) REVERT: I 62 PHE cc_start: 0.6970 (m-80) cc_final: 0.6456 (m-80) REVERT: I 124 GLU cc_start: 0.7156 (tt0) cc_final: 0.6707 (mp0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1633 time to fit residues: 41.8873 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 : 0.944 ------------------------------------------------------------------------------- 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: 0.6980 chunk 327 optimal weight: 9.9990 chunk 118 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 364 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.125514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082672 restraints weight = 90620.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084071 restraints weight = 76046.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084118 restraints weight = 59029.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084240 restraints weight = 57282.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084428 restraints weight = 54150.781| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2960 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= 0.112 Angle : 0.598 15.691 45015 Z= 0.298 Chirality : 0.046 0.364 5225 Planarity : 0.004 0.076 5694 Dihedral : 6.308 56.980 5453 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.91 (0.13), residues: 3987 helix: 0.14 (0.20), residues: 726 sheet: 0.25 (0.16), residues: 1015 loop : -1.29 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 143 TYR 0.025 0.001 TYR B 495 PHE 0.020 0.001 PHE B 906 TRP 0.015 0.001 TRP D 97 HIS 0.004 0.001 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00243 (32887) covalent geometry : angle 0.57898 (44757) SS BOND : bond 0.00378 ( 48) SS BOND : angle 1.30587 ( 96) hydrogen bonds : bond 0.04806 ( 1069) hydrogen bonds : angle 4.86082 ( 2847) Misc. bond : bond 0.01097 ( 1) link_BETA1-4 : bond 0.00757 ( 13) link_BETA1-4 : angle 2.98115 ( 39) link_NAG-ASN : bond 0.00530 ( 41) link_NAG-ASN : angle 2.17615 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.58 seconds wall clock time: 73 minutes 59.83 seconds (4439.83 seconds total)