Starting phenix.real_space_refine on Sat Jun 21 16:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzi_37953/06_2025/8wzi_37953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzi_37953/06_2025/8wzi_37953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzi_37953/06_2025/8wzi_37953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzi_37953/06_2025/8wzi_37953.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzi_37953/06_2025/8wzi_37953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzi_37953/06_2025/8wzi_37953.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 108 5.16 5 C 15891 2.51 5 N 4065 2.21 5 O 4907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24971 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8008 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 47, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8008 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 47, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8008 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 47, 'TRANS': 978} Chain breaks: 7 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "W" 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: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.95, per 1000 atoms: 0.60 Number of scatterers: 24971 At special positions: 0 Unit cell: (140.17, 170.13, 148.73, 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 108 16.00 O 4907 8.00 N 4065 7.00 C 15891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.01 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.02 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.04 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.02 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 706 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 714 " " NAG J 1 " - " ASN A 798 " " NAG K 1 " - " ASN A1071 " " NAG L 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG O 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 714 " " NAG T 1 " - " ASN B 798 " " NAG U 1 " - " ASN B1071 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 616 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 36 sheets defined 26.2% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.061A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.729A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.884A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.807A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.847A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 removed outlier: 3.552A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 753 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.846A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.522A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.519A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.121A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.545A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.578A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.213A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.620A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 753 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 846 through 853 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.843A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.531A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.512A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.652A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.813A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.248A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.749A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.675A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.840A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 753 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 846 through 853 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.840A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.524A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.519A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.616A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.266A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.196A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.253A 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: 5.742A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.714A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 172 removed outlier: 5.105A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.572A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.644A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.552A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.512A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 699 through 700 Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.706A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1044 through 1047 removed outlier: 7.074A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.345A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.524A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.690A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 172 removed outlier: 5.427A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.530A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.623A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.636A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 453 removed outlier: 4.015A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.514A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AC5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.708A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1044 through 1047 removed outlier: 7.066A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.344A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.521A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.714A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 163 through 172 removed outlier: 5.886A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.662A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 355 through 356 Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.491A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.689A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1044 through 1047 removed outlier: 7.074A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.338A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1117 through 1119 980 hydrogen bonds defined for protein. 2754 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: 11.26 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4015 1.31 - 1.45: 7237 1.45 - 1.58: 14127 1.58 - 1.71: 0 1.71 - 1.84: 135 Bond restraints: 25514 Sorted by residual: bond pdb=" C VAL B 988 " pdb=" O VAL B 988 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.29e-02 6.01e+03 2.00e+01 bond pdb=" C SER B 116 " pdb=" O SER B 116 " ideal model delta sigma weight residual 1.234 1.288 -0.054 1.22e-02 6.72e+03 1.96e+01 bond pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 1.453 1.492 -0.039 9.20e-03 1.18e+04 1.76e+01 bond pdb=" C PRO B 984 " pdb=" O PRO B 984 " ideal model delta sigma weight residual 1.237 1.184 0.054 1.32e-02 5.74e+03 1.65e+01 bond pdb=" N ILE C 468 " pdb=" CA ILE C 468 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.56e+01 ... (remaining 25509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 22708 1.49 - 2.99: 10190 2.99 - 4.48: 1671 4.48 - 5.98: 127 5.98 - 7.47: 19 Bond angle restraints: 34715 Sorted by residual: angle pdb=" CA ASP C 976 " pdb=" CB ASP C 976 " pdb=" CG ASP C 976 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 117.72 -7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N PRO C 983 " pdb=" CA PRO C 983 " pdb=" C PRO C 983 " ideal model delta sigma weight residual 110.70 117.23 -6.53 1.22e+00 6.72e-01 2.87e+01 angle pdb=" C VAL C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 121.61 125.67 -4.06 7.70e-01 1.69e+00 2.78e+01 angle pdb=" C PHE C 565 " pdb=" N GLY C 566 " pdb=" CA GLY C 566 " ideal model delta sigma weight residual 122.33 126.04 -3.71 7.30e-01 1.88e+00 2.58e+01 ... (remaining 34710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 15025 25.00 - 50.01: 861 50.01 - 75.01: 116 75.01 - 100.02: 36 100.02 - 125.02: 7 Dihedral angle restraints: 16045 sinusoidal: 7090 harmonic: 8955 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -1.73 -84.27 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 9.78 83.22 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A1079 " pdb=" SG CYS A1079 " pdb=" SG CYS A1123 " pdb=" CB CYS A1123 " ideal model delta sinusoidal sigma weight residual -86.00 -16.47 -69.53 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 16042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2632 0.076 - 0.152: 1294 0.152 - 0.229: 216 0.229 - 0.305: 15 0.305 - 0.381: 3 Chirality restraints: 4160 Sorted by residual: chirality pdb=" C1 MAN T 3 " pdb=" O4 NAG T 2 " pdb=" C2 MAN T 3 " pdb=" O5 MAN T 3 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.23e+01 chirality pdb=" C1 MAN c 3 " pdb=" O4 NAG c 2 " pdb=" C2 MAN c 3 " pdb=" O5 MAN c 3 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.69e+01 ... (remaining 4157 not shown) Planarity restraints: 4424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 738 " -0.059 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR A 738 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 738 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 738 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 738 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 738 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 738 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 738 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 532 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" CG ASN B 532 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 532 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 532 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1104 " 0.019 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C ARG B1104 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG B1104 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B1105 " 0.024 2.00e-02 2.50e+03 ... (remaining 4421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1535 2.74 - 3.28: 25242 3.28 - 3.82: 38915 3.82 - 4.36: 50335 4.36 - 4.90: 81817 Nonbonded interactions: 197844 Sorted by model distance: nonbonded pdb=" O GLN C 962 " pdb=" OG SER C 965 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B1113 " pdb=" OD1 ASP B1115 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 800 " pdb=" OE1 GLN B 801 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.250 3.040 nonbonded pdb=" O GLY C 601 " pdb=" OG1 THR C 604 " model vdw 2.263 3.040 ... (remaining 197839 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'g' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 59.570 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:15.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.013 0.058 25621 Z= 0.947 Angle : 1.574 11.803 34997 Z= 1.124 Chirality : 0.081 0.381 4160 Planarity : 0.007 0.042 4383 Dihedral : 15.506 125.024 10162 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 3.25 % Allowed : 13.94 % Favored : 82.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3030 helix: 1.11 (0.19), residues: 680 sheet: -0.13 (0.19), residues: 633 loop : -1.41 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP A 104 HIS 0.038 0.005 HIS A 49 PHE 0.057 0.006 PHE A 194 TYR 0.059 0.007 TYR A 738 ARG 0.034 0.003 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 41) link_NAG-ASN : angle 3.31698 ( 123) link_ALPHA1-4 : bond 0.00205 ( 5) link_ALPHA1-4 : angle 3.42930 ( 15) link_BETA1-4 : bond 0.00505 ( 21) link_BETA1-4 : angle 2.20253 ( 63) hydrogen bonds : bond 0.11666 ( 980) hydrogen bonds : angle 7.05938 ( 2754) link_BETA1-6 : bond 0.00048 ( 1) link_BETA1-6 : angle 3.94760 ( 3) SS BOND : bond 0.01251 ( 39) SS BOND : angle 2.74935 ( 78) covalent geometry : bond 0.01288 (25514) covalent geometry : angle 1.55756 (34715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 209 time to evaluate : 2.568 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 210 ILE cc_start: 0.7684 (mp) cc_final: 0.7292 (pp) REVERT: A 309 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7294 (tm-30) REVERT: A 532 ASN cc_start: 0.8921 (t0) cc_final: 0.8454 (t0) REVERT: B 52 GLN cc_start: 0.6985 (tm130) cc_final: 0.6782 (tm130) REVERT: B 177 MET cc_start: 0.7321 (pmm) cc_final: 0.4728 (mmm) REVERT: B 195 LYS cc_start: 0.7294 (mttt) cc_final: 0.7064 (mttt) REVERT: B 275 PHE cc_start: 0.8075 (m-80) cc_final: 0.7871 (m-10) REVERT: B 309 GLU cc_start: 0.8020 (tp30) cc_final: 0.7778 (mm-30) REVERT: B 464 PHE cc_start: 0.8491 (m-10) cc_final: 0.8189 (m-80) REVERT: B 515 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6186 (p90) REVERT: B 975 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7947 (t0) REVERT: C 168 PHE cc_start: 0.7031 (m-80) cc_final: 0.6830 (m-80) outliers start: 87 outliers final: 46 residues processed: 285 average time/residue: 0.8372 time to fit residues: 300.2873 Evaluate side-chains 214 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 822 LYS Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN C 66 HIS C 207 HIS C 506 GLN C 898 GLN C 999 GLN C1007 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.147977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098198 restraints weight = 56371.086| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.45 r_work: 0.3326 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25621 Z= 0.126 Angle : 0.625 12.633 34997 Z= 0.313 Chirality : 0.044 0.264 4160 Planarity : 0.003 0.049 4383 Dihedral : 10.212 112.518 4798 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 3.25 % Allowed : 15.25 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3030 helix: 1.57 (0.20), residues: 684 sheet: 0.07 (0.18), residues: 693 loop : -1.25 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS B1045 PHE 0.025 0.001 PHE C 55 TYR 0.020 0.001 TYR C 369 ARG 0.003 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 41) link_NAG-ASN : angle 2.65399 ( 123) link_ALPHA1-4 : bond 0.01440 ( 5) link_ALPHA1-4 : angle 2.55992 ( 15) link_BETA1-4 : bond 0.00428 ( 21) link_BETA1-4 : angle 1.56269 ( 63) hydrogen bonds : bond 0.04289 ( 980) hydrogen bonds : angle 5.86679 ( 2754) link_BETA1-6 : bond 0.00984 ( 1) link_BETA1-6 : angle 1.79219 ( 3) SS BOND : bond 0.00490 ( 39) SS BOND : angle 1.46558 ( 78) covalent geometry : bond 0.00266 (25514) covalent geometry : angle 0.59713 (34715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 193 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.8213 (mp) cc_final: 0.7832 (pp) REVERT: A 226 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 309 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7569 (tm-30) REVERT: A 351 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8377 (p90) REVERT: A 356 LYS cc_start: 0.8870 (pptt) cc_final: 0.8602 (pptt) REVERT: A 532 ASN cc_start: 0.9246 (t0) cc_final: 0.8798 (t0) REVERT: A 975 ASN cc_start: 0.9312 (t0) cc_final: 0.8951 (t0) REVERT: A 1104 ARG cc_start: 0.8193 (mpt-90) cc_final: 0.7879 (mpt-90) REVERT: A 1108 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 177 MET cc_start: 0.7511 (pmm) cc_final: 0.5250 (mmm) REVERT: B 309 GLU cc_start: 0.8197 (tp30) cc_final: 0.7942 (mm-30) REVERT: B 319 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8074 (tpp80) REVERT: B 515 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.6245 (p90) REVERT: B 564 GLN cc_start: 0.7299 (tp40) cc_final: 0.6770 (pt0) REVERT: B 975 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 1108 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 116 SER cc_start: 0.5676 (t) cc_final: 0.5342 (p) REVERT: C 168 PHE cc_start: 0.8468 (m-80) cc_final: 0.8098 (m-80) REVERT: C 317 ASN cc_start: 0.7894 (m-40) cc_final: 0.7334 (m-40) REVERT: C 985 GLU cc_start: 0.8268 (pm20) cc_final: 0.8047 (pm20) outliers start: 87 outliers final: 42 residues processed: 271 average time/residue: 0.8631 time to fit residues: 292.8382 Evaluate side-chains 206 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 49 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 216 optimal weight: 0.0980 chunk 167 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 204 optimal weight: 20.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN A 759 GLN A1020 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 748 ASN C 999 GLN C1020 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.145078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094212 restraints weight = 56427.721| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.43 r_work: 0.3241 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25621 Z= 0.232 Angle : 0.650 12.893 34997 Z= 0.327 Chirality : 0.046 0.222 4160 Planarity : 0.004 0.056 4383 Dihedral : 9.649 114.277 4770 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.51 % Allowed : 15.96 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3030 helix: 1.12 (0.20), residues: 684 sheet: 0.03 (0.19), residues: 690 loop : -1.29 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 436 HIS 0.003 0.001 HIS C1080 PHE 0.018 0.001 PHE A1086 TYR 0.023 0.002 TYR A1064 ARG 0.007 0.001 ARG C 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 41) link_NAG-ASN : angle 2.59024 ( 123) link_ALPHA1-4 : bond 0.01433 ( 5) link_ALPHA1-4 : angle 2.69600 ( 15) link_BETA1-4 : bond 0.00221 ( 21) link_BETA1-4 : angle 1.54636 ( 63) hydrogen bonds : bond 0.04606 ( 980) hydrogen bonds : angle 5.91578 ( 2754) link_BETA1-6 : bond 0.01163 ( 1) link_BETA1-6 : angle 2.61912 ( 3) SS BOND : bond 0.00489 ( 39) SS BOND : angle 1.61903 ( 78) covalent geometry : bond 0.00522 (25514) covalent geometry : angle 0.62325 (34715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 181 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 351 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8432 (p90) REVERT: A 356 LYS cc_start: 0.8903 (pptt) cc_final: 0.8540 (pptt) REVERT: A 392 PHE cc_start: 0.8096 (m-10) cc_final: 0.7634 (m-80) REVERT: A 532 ASN cc_start: 0.9417 (t0) cc_final: 0.8993 (t0) REVERT: A 975 ASN cc_start: 0.9337 (t0) cc_final: 0.8970 (t0) REVERT: A 1108 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 58 PHE cc_start: 0.9067 (m-80) cc_final: 0.8782 (m-80) REVERT: B 120 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8460 (m) REVERT: B 273 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6803 (mmm-85) REVERT: B 309 GLU cc_start: 0.8299 (tp30) cc_final: 0.8070 (mm-30) REVERT: B 453 TYR cc_start: 0.6740 (p90) cc_final: 0.6206 (p90) REVERT: B 515 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.6884 (p90) REVERT: B 748 ASN cc_start: 0.8750 (m110) cc_final: 0.8527 (m-40) REVERT: B 975 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8535 (t0) REVERT: C 229 LEU cc_start: 0.9114 (mm) cc_final: 0.8579 (tm) REVERT: C 985 GLU cc_start: 0.8273 (pm20) cc_final: 0.7874 (pm20) outliers start: 94 outliers final: 48 residues processed: 260 average time/residue: 0.8119 time to fit residues: 267.4935 Evaluate side-chains 212 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 20.0000 chunk 280 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 157 optimal weight: 7.9990 chunk 243 optimal weight: 40.0000 chunk 161 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.144676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093695 restraints weight = 56753.545| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.45 r_work: 0.3235 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25621 Z= 0.217 Angle : 0.644 12.801 34997 Z= 0.322 Chirality : 0.046 0.214 4160 Planarity : 0.004 0.057 4383 Dihedral : 9.279 113.407 4762 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 3.92 % Allowed : 16.97 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3030 helix: 0.96 (0.20), residues: 685 sheet: -0.05 (0.19), residues: 692 loop : -1.29 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.003 0.001 HIS C1080 PHE 0.026 0.001 PHE C 168 TYR 0.022 0.001 TYR A1064 ARG 0.015 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 41) link_NAG-ASN : angle 2.54329 ( 123) link_ALPHA1-4 : bond 0.01466 ( 5) link_ALPHA1-4 : angle 2.78437 ( 15) link_BETA1-4 : bond 0.00267 ( 21) link_BETA1-4 : angle 1.46299 ( 63) hydrogen bonds : bond 0.04433 ( 980) hydrogen bonds : angle 5.88219 ( 2754) link_BETA1-6 : bond 0.01851 ( 1) link_BETA1-6 : angle 1.81109 ( 3) SS BOND : bond 0.00445 ( 39) SS BOND : angle 1.81787 ( 78) covalent geometry : bond 0.00484 (25514) covalent geometry : angle 0.61668 (34715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 176 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8415 (p90) REVERT: A 392 PHE cc_start: 0.8115 (m-10) cc_final: 0.7774 (m-80) REVERT: A 452 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7627 (mm) REVERT: A 532 ASN cc_start: 0.9423 (t0) cc_final: 0.8997 (t0) REVERT: A 973 VAL cc_start: 0.7546 (p) cc_final: 0.7161 (m) REVERT: A 1108 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 58 PHE cc_start: 0.9083 (m-80) cc_final: 0.8804 (m-80) REVERT: B 233 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4794 (pt) REVERT: B 273 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6807 (mmm-85) REVERT: B 453 TYR cc_start: 0.6588 (p90) cc_final: 0.5772 (p90) REVERT: B 515 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6814 (p90) REVERT: B 748 ASN cc_start: 0.8792 (m110) cc_final: 0.8569 (m-40) REVERT: B 975 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8493 (t0) REVERT: C 229 LEU cc_start: 0.9115 (mm) cc_final: 0.8564 (tm) outliers start: 105 outliers final: 51 residues processed: 266 average time/residue: 0.7718 time to fit residues: 263.5693 Evaluate side-chains 221 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 266 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 246 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 278 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 204 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B1020 ASN C 207 HIS C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093769 restraints weight = 56303.188| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.44 r_work: 0.3236 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25621 Z= 0.205 Angle : 0.642 12.793 34997 Z= 0.321 Chirality : 0.045 0.212 4160 Planarity : 0.004 0.058 4383 Dihedral : 9.076 113.698 4762 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 3.36 % Allowed : 18.27 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3030 helix: 0.91 (0.20), residues: 685 sheet: -0.11 (0.19), residues: 699 loop : -1.30 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 436 HIS 0.003 0.001 HIS C1080 PHE 0.017 0.001 PHE C 55 TYR 0.021 0.001 TYR A1064 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 41) link_NAG-ASN : angle 2.48953 ( 123) link_ALPHA1-4 : bond 0.01413 ( 5) link_ALPHA1-4 : angle 2.82659 ( 15) link_BETA1-4 : bond 0.00217 ( 21) link_BETA1-4 : angle 1.43893 ( 63) hydrogen bonds : bond 0.04412 ( 980) hydrogen bonds : angle 5.85148 ( 2754) link_BETA1-6 : bond 0.01160 ( 1) link_BETA1-6 : angle 1.28411 ( 3) SS BOND : bond 0.00485 ( 39) SS BOND : angle 1.75041 ( 78) covalent geometry : bond 0.00456 (25514) covalent geometry : angle 0.61537 (34715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 172 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (p90) REVERT: A 392 PHE cc_start: 0.8071 (m-10) cc_final: 0.7855 (m-80) REVERT: A 441 LEU cc_start: 0.9391 (mm) cc_final: 0.9019 (pp) REVERT: A 452 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7557 (mm) REVERT: A 532 ASN cc_start: 0.9418 (t0) cc_final: 0.8978 (t0) REVERT: A 852 PHE cc_start: 0.7231 (m-80) cc_final: 0.6852 (m-80) REVERT: A 1108 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 58 PHE cc_start: 0.9104 (m-80) cc_final: 0.8821 (m-80) REVERT: B 195 LYS cc_start: 0.7838 (mttt) cc_final: 0.7618 (mttt) REVERT: B 233 ILE cc_start: 0.5257 (OUTLIER) cc_final: 0.4775 (pt) REVERT: B 273 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6810 (mmm-85) REVERT: B 453 TYR cc_start: 0.6361 (p90) cc_final: 0.5905 (p90) REVERT: B 515 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6709 (p90) REVERT: B 748 ASN cc_start: 0.8807 (m110) cc_final: 0.8584 (m-40) REVERT: B 909 THR cc_start: 0.8520 (m) cc_final: 0.8236 (t) REVERT: B 985 GLU cc_start: 0.8642 (pm20) cc_final: 0.8420 (pm20) REVERT: C 229 LEU cc_start: 0.9141 (mm) cc_final: 0.8565 (tm) REVERT: C 317 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7635 (m-40) REVERT: C 589 PRO cc_start: 0.8289 (Cg_exo) cc_final: 0.8088 (Cg_endo) REVERT: C 985 GLU cc_start: 0.8374 (pm20) cc_final: 0.8116 (pm20) outliers start: 90 outliers final: 56 residues processed: 249 average time/residue: 0.7838 time to fit residues: 251.6717 Evaluate side-chains 223 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 166 optimal weight: 0.2980 chunk 162 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 59 optimal weight: 0.0050 chunk 153 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 232 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 207 HIS ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.146618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096245 restraints weight = 56414.536| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.45 r_work: 0.3280 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25621 Z= 0.122 Angle : 0.609 12.758 34997 Z= 0.301 Chirality : 0.044 0.220 4160 Planarity : 0.004 0.058 4383 Dihedral : 8.629 110.419 4758 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 3.03 % Allowed : 19.10 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3030 helix: 1.09 (0.20), residues: 686 sheet: 0.01 (0.19), residues: 689 loop : -1.28 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 104 HIS 0.002 0.000 HIS A1085 PHE 0.021 0.001 PHE B 201 TYR 0.018 0.001 TYR A1064 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 41) link_NAG-ASN : angle 2.38533 ( 123) link_ALPHA1-4 : bond 0.01450 ( 5) link_ALPHA1-4 : angle 2.85697 ( 15) link_BETA1-4 : bond 0.00318 ( 21) link_BETA1-4 : angle 1.28862 ( 63) hydrogen bonds : bond 0.03983 ( 980) hydrogen bonds : angle 5.61935 ( 2754) link_BETA1-6 : bond 0.01127 ( 1) link_BETA1-6 : angle 1.10160 ( 3) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.67460 ( 78) covalent geometry : bond 0.00263 (25514) covalent geometry : angle 0.58332 (34715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 179 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.8361 (mp) cc_final: 0.7978 (pp) REVERT: A 351 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8368 (p90) REVERT: A 392 PHE cc_start: 0.8090 (m-10) cc_final: 0.7779 (m-80) REVERT: A 441 LEU cc_start: 0.9355 (mm) cc_final: 0.8981 (pp) REVERT: A 452 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7549 (mm) REVERT: A 532 ASN cc_start: 0.9423 (t0) cc_final: 0.8984 (t0) REVERT: A 852 PHE cc_start: 0.7162 (m-80) cc_final: 0.6799 (m-80) REVERT: A 1108 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 233 ILE cc_start: 0.5136 (OUTLIER) cc_final: 0.4459 (pt) REVERT: B 453 TYR cc_start: 0.6503 (p90) cc_final: 0.6060 (p90) REVERT: B 515 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.6388 (p90) REVERT: B 748 ASN cc_start: 0.8775 (m110) cc_final: 0.8547 (m-40) REVERT: B 975 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8273 (t0) REVERT: B 985 GLU cc_start: 0.8634 (pm20) cc_final: 0.8408 (pm20) REVERT: C 55 PHE cc_start: 0.7825 (m-80) cc_final: 0.7573 (m-80) REVERT: C 177 MET cc_start: 0.7560 (mmp) cc_final: 0.7168 (mmp) REVERT: C 229 LEU cc_start: 0.9103 (mm) cc_final: 0.8535 (tm) REVERT: C 519 HIS cc_start: 0.2810 (OUTLIER) cc_final: 0.2427 (t-90) REVERT: C 985 GLU cc_start: 0.8344 (pm20) cc_final: 0.8074 (pm20) outliers start: 81 outliers final: 47 residues processed: 248 average time/residue: 0.8652 time to fit residues: 269.9360 Evaluate side-chains 207 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 115 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 289 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 232 optimal weight: 40.0000 chunk 260 optimal weight: 0.6980 chunk 238 optimal weight: 0.0470 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.145114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094221 restraints weight = 56845.296| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.46 r_work: 0.3255 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25621 Z= 0.199 Angle : 0.639 12.834 34997 Z= 0.318 Chirality : 0.045 0.214 4160 Planarity : 0.004 0.057 4383 Dihedral : 8.577 112.099 4757 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 3.36 % Allowed : 18.91 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3030 helix: 1.01 (0.20), residues: 685 sheet: -0.08 (0.19), residues: 714 loop : -1.30 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 436 HIS 0.003 0.001 HIS B1080 PHE 0.015 0.001 PHE C1118 TYR 0.026 0.002 TYR A 380 ARG 0.008 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 41) link_NAG-ASN : angle 2.41036 ( 123) link_ALPHA1-4 : bond 0.01455 ( 5) link_ALPHA1-4 : angle 2.94785 ( 15) link_BETA1-4 : bond 0.00198 ( 21) link_BETA1-4 : angle 1.36925 ( 63) hydrogen bonds : bond 0.04255 ( 980) hydrogen bonds : angle 5.71360 ( 2754) link_BETA1-6 : bond 0.00684 ( 1) link_BETA1-6 : angle 1.23120 ( 3) SS BOND : bond 0.00545 ( 39) SS BOND : angle 1.81531 ( 78) covalent geometry : bond 0.00445 (25514) covalent geometry : angle 0.61336 (34715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 163 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8372 (p90) REVERT: A 441 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8896 (pp) REVERT: A 452 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 532 ASN cc_start: 0.9498 (t0) cc_final: 0.9084 (t0) REVERT: A 852 PHE cc_start: 0.7222 (m-80) cc_final: 0.7021 (m-80) REVERT: A 1108 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 233 ILE cc_start: 0.4958 (OUTLIER) cc_final: 0.4115 (pt) REVERT: B 453 TYR cc_start: 0.6322 (p90) cc_final: 0.5856 (p90) REVERT: B 515 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6574 (p90) REVERT: B 748 ASN cc_start: 0.8782 (m110) cc_final: 0.8551 (m-40) REVERT: B 909 THR cc_start: 0.8531 (m) cc_final: 0.8268 (t) REVERT: B 985 GLU cc_start: 0.8606 (pm20) cc_final: 0.8406 (pm20) REVERT: C 229 LEU cc_start: 0.9142 (mm) cc_final: 0.8576 (tm) REVERT: C 519 HIS cc_start: 0.2327 (OUTLIER) cc_final: 0.1976 (t-90) REVERT: C 985 GLU cc_start: 0.8344 (pm20) cc_final: 0.7975 (pm20) outliers start: 90 outliers final: 57 residues processed: 237 average time/residue: 0.8399 time to fit residues: 253.3464 Evaluate side-chains 218 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 106 optimal weight: 30.0000 chunk 132 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 143 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.144796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094030 restraints weight = 56637.270| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.50 r_work: 0.3246 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25621 Z= 0.200 Angle : 0.654 12.776 34997 Z= 0.324 Chirality : 0.046 0.225 4160 Planarity : 0.004 0.058 4383 Dihedral : 8.466 112.459 4757 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.18 % Allowed : 19.47 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3030 helix: 0.93 (0.20), residues: 686 sheet: -0.11 (0.18), residues: 723 loop : -1.32 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 436 HIS 0.003 0.001 HIS B1045 PHE 0.026 0.001 PHE B 201 TYR 0.021 0.001 TYR A1064 ARG 0.007 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 41) link_NAG-ASN : angle 2.41781 ( 123) link_ALPHA1-4 : bond 0.01517 ( 5) link_ALPHA1-4 : angle 3.00229 ( 15) link_BETA1-4 : bond 0.00196 ( 21) link_BETA1-4 : angle 1.34275 ( 63) hydrogen bonds : bond 0.04274 ( 980) hydrogen bonds : angle 5.74177 ( 2754) link_BETA1-6 : bond 0.00511 ( 1) link_BETA1-6 : angle 1.30306 ( 3) SS BOND : bond 0.00551 ( 39) SS BOND : angle 1.79284 ( 78) covalent geometry : bond 0.00446 (25514) covalent geometry : angle 0.62900 (34715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 163 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.2293 (OUTLIER) cc_final: 0.0276 (t-90) REVERT: A 351 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (p90) REVERT: A 441 LEU cc_start: 0.9330 (mm) cc_final: 0.8923 (pp) REVERT: A 452 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7590 (mm) REVERT: A 532 ASN cc_start: 0.9473 (t0) cc_final: 0.9062 (t0) REVERT: A 852 PHE cc_start: 0.7234 (m-80) cc_final: 0.7026 (m-80) REVERT: A 1108 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 233 ILE cc_start: 0.4779 (OUTLIER) cc_final: 0.4380 (pt) REVERT: B 453 TYR cc_start: 0.6687 (p90) cc_final: 0.6261 (p90) REVERT: B 515 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6627 (p90) REVERT: B 748 ASN cc_start: 0.8834 (m110) cc_final: 0.8630 (m-40) REVERT: B 909 THR cc_start: 0.8557 (m) cc_final: 0.8294 (t) REVERT: B 975 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8332 (t0) REVERT: C 229 LEU cc_start: 0.9140 (mm) cc_final: 0.8491 (tm) REVERT: C 519 HIS cc_start: 0.2293 (OUTLIER) cc_final: 0.1928 (t-90) REVERT: C 985 GLU cc_start: 0.8330 (pm20) cc_final: 0.7947 (pm20) outliers start: 85 outliers final: 61 residues processed: 236 average time/residue: 0.7881 time to fit residues: 240.2925 Evaluate side-chains 226 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 252 optimal weight: 2.9990 chunk 246 optimal weight: 40.0000 chunk 99 optimal weight: 0.8980 chunk 281 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 37 optimal weight: 40.0000 chunk 156 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.145303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094622 restraints weight = 56501.795| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.47 r_work: 0.3269 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25621 Z= 0.157 Angle : 0.637 12.736 34997 Z= 0.315 Chirality : 0.045 0.218 4160 Planarity : 0.004 0.057 4383 Dihedral : 8.264 111.590 4756 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 2.77 % Allowed : 20.07 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3030 helix: 0.98 (0.20), residues: 686 sheet: -0.06 (0.19), residues: 716 loop : -1.31 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 104 HIS 0.003 0.001 HIS B1045 PHE 0.016 0.001 PHE A 392 TYR 0.020 0.001 TYR C 901 ARG 0.006 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 41) link_NAG-ASN : angle 2.38503 ( 123) link_ALPHA1-4 : bond 0.01558 ( 5) link_ALPHA1-4 : angle 3.06328 ( 15) link_BETA1-4 : bond 0.00232 ( 21) link_BETA1-4 : angle 1.28498 ( 63) hydrogen bonds : bond 0.04111 ( 980) hydrogen bonds : angle 5.66567 ( 2754) link_BETA1-6 : bond 0.00656 ( 1) link_BETA1-6 : angle 1.30949 ( 3) SS BOND : bond 0.00443 ( 39) SS BOND : angle 1.61772 ( 78) covalent geometry : bond 0.00346 (25514) covalent geometry : angle 0.61296 (34715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.8432 (mp) cc_final: 0.8032 (pp) REVERT: A 245 HIS cc_start: 0.2237 (OUTLIER) cc_final: 0.0287 (t-90) REVERT: A 441 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8864 (pp) REVERT: A 532 ASN cc_start: 0.9523 (t0) cc_final: 0.9129 (t0) REVERT: A 1108 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 233 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4411 (pt) REVERT: B 453 TYR cc_start: 0.6644 (p90) cc_final: 0.6237 (p90) REVERT: B 515 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6413 (p90) REVERT: B 748 ASN cc_start: 0.8788 (m110) cc_final: 0.8560 (m-40) REVERT: B 909 THR cc_start: 0.8528 (m) cc_final: 0.8260 (t) REVERT: B 975 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8324 (t0) REVERT: B 1104 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7310 (mtt90) REVERT: C 197 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6383 (pt) REVERT: C 519 HIS cc_start: 0.2129 (OUTLIER) cc_final: 0.1775 (t-90) REVERT: C 985 GLU cc_start: 0.8328 (pm20) cc_final: 0.7983 (pm20) outliers start: 74 outliers final: 57 residues processed: 230 average time/residue: 0.7760 time to fit residues: 227.5293 Evaluate side-chains 218 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 993 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 284 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 289 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 209 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.145395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094810 restraints weight = 55809.121| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.44 r_work: 0.3271 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25621 Z= 0.157 Angle : 0.641 12.740 34997 Z= 0.316 Chirality : 0.045 0.218 4160 Planarity : 0.004 0.057 4383 Dihedral : 8.023 111.330 4753 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 2.54 % Allowed : 20.40 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3030 helix: 1.02 (0.20), residues: 687 sheet: -0.06 (0.19), residues: 699 loop : -1.30 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 436 HIS 0.002 0.001 HIS B1045 PHE 0.032 0.001 PHE B 201 TYR 0.027 0.001 TYR C 901 ARG 0.006 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 41) link_NAG-ASN : angle 2.35651 ( 123) link_ALPHA1-4 : bond 0.01633 ( 5) link_ALPHA1-4 : angle 3.15394 ( 15) link_BETA1-4 : bond 0.00237 ( 21) link_BETA1-4 : angle 1.26149 ( 63) hydrogen bonds : bond 0.04069 ( 980) hydrogen bonds : angle 5.63325 ( 2754) link_BETA1-6 : bond 0.00533 ( 1) link_BETA1-6 : angle 1.28934 ( 3) SS BOND : bond 0.00521 ( 39) SS BOND : angle 1.64941 ( 78) covalent geometry : bond 0.00347 (25514) covalent geometry : angle 0.61700 (34715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 162 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6277 (pp) REVERT: A 210 ILE cc_start: 0.8469 (mp) cc_final: 0.8074 (pp) REVERT: A 245 HIS cc_start: 0.2397 (OUTLIER) cc_final: 0.0349 (t-90) REVERT: A 441 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8862 (pp) REVERT: A 532 ASN cc_start: 0.9472 (t0) cc_final: 0.9052 (t0) REVERT: A 1108 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 233 ILE cc_start: 0.4746 (OUTLIER) cc_final: 0.4362 (pt) REVERT: B 453 TYR cc_start: 0.6571 (p90) cc_final: 0.6163 (p90) REVERT: B 515 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.6544 (p90) REVERT: B 748 ASN cc_start: 0.8777 (m110) cc_final: 0.8549 (m-40) REVERT: B 909 THR cc_start: 0.8531 (m) cc_final: 0.8207 (t) REVERT: B 975 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8323 (t0) REVERT: B 1104 ARG cc_start: 0.7832 (mpt180) cc_final: 0.7577 (mtt90) REVERT: C 197 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6446 (pt) REVERT: C 229 LEU cc_start: 0.9057 (mm) cc_final: 0.8503 (tm) REVERT: C 318 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.7960 (p90) REVERT: C 519 HIS cc_start: 0.2146 (OUTLIER) cc_final: 0.1786 (t-90) REVERT: C 985 GLU cc_start: 0.8307 (pm20) cc_final: 0.7949 (pm20) outliers start: 68 outliers final: 58 residues processed: 222 average time/residue: 0.8707 time to fit residues: 246.1819 Evaluate side-chains 220 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 993 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 280 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 56 optimal weight: 0.0970 chunk 5 optimal weight: 20.0000 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.146109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095708 restraints weight = 55885.874| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.47 r_work: 0.3276 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25621 Z= 0.132 Angle : 0.634 12.718 34997 Z= 0.312 Chirality : 0.044 0.222 4160 Planarity : 0.004 0.057 4383 Dihedral : 7.721 110.198 4753 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.77 % Allowed : 20.14 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3030 helix: 1.08 (0.20), residues: 687 sheet: 0.01 (0.19), residues: 697 loop : -1.29 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 436 HIS 0.003 0.001 HIS B1045 PHE 0.015 0.001 PHE A 464 TYR 0.024 0.001 TYR B 901 ARG 0.006 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 41) link_NAG-ASN : angle 2.30886 ( 123) link_ALPHA1-4 : bond 0.01704 ( 5) link_ALPHA1-4 : angle 3.27779 ( 15) link_BETA1-4 : bond 0.00275 ( 21) link_BETA1-4 : angle 1.20347 ( 63) hydrogen bonds : bond 0.03938 ( 980) hydrogen bonds : angle 5.55603 ( 2754) link_BETA1-6 : bond 0.00610 ( 1) link_BETA1-6 : angle 1.25184 ( 3) SS BOND : bond 0.00472 ( 39) SS BOND : angle 1.74960 ( 78) covalent geometry : bond 0.00286 (25514) covalent geometry : angle 0.60988 (34715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18463.49 seconds wall clock time: 315 minutes 34.85 seconds (18934.85 seconds total)