Starting phenix.real_space_refine on Fri Feb 6 22:32:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy7_25519/02_2026/7sy7_25519.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy7_25519/02_2026/7sy7_25519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy7_25519/02_2026/7sy7_25519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy7_25519/02_2026/7sy7_25519.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy7_25519/02_2026/7sy7_25519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy7_25519/02_2026/7sy7_25519.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 132 5.16 5 C 18199 2.51 5 N 4671 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28581 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "B" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.84, per 1000 atoms: 0.20 Number of scatterers: 28581 At special positions: 0 Unit cell: (140, 156, 237, 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 132 16.00 O 5579 8.00 N 4671 7.00 C 18199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 42 sheets defined 33.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.900A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.630A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.961A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.558A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.301A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.226A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.340A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.668A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.096A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.602A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.927A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.998A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.820A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.772A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.912A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.583A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.547A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.585A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.541A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.891A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.100A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.064A pdb=" N ASN E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.618A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.756A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.045A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.914A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.683A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.712A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.793A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.590A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.672A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.256A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.599A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.335A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.503A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.689A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.449A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.900A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.368A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.538A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.165A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.933A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.494A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.082A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.106A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.601A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.890A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.308A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.945A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.319A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.014A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 11.474A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.566A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.726A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.858A 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: 5.165A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.052A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.066A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.824A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.948A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 5.966A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.151A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 154 through 163 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 163 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.698A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.617A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.895A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.604A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.911A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.358A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.503A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.056A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.348A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9011 1.34 - 1.47: 7374 1.47 - 1.59: 12676 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 29241 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.51e-02 4.39e+03 1.31e+01 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 29236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 38603 2.20 - 4.40: 1076 4.40 - 6.61: 78 6.61 - 8.81: 31 8.81 - 11.01: 3 Bond angle restraints: 39791 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.43 -5.73 1.22e+00 6.72e-01 2.21e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.06e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 128.59 -6.13 1.41e+00 5.03e-01 1.89e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.97 -5.27 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.31 -8.21 2.00e+00 2.50e-01 1.69e+01 ... (remaining 39786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16785 17.95 - 35.89: 1178 35.89 - 53.84: 189 53.84 - 71.78: 57 71.78 - 89.73: 35 Dihedral angle restraints: 18244 sinusoidal: 7996 harmonic: 10248 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -46.03 -39.97 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 18241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3665 0.067 - 0.135: 860 0.135 - 0.202: 122 0.202 - 0.269: 7 0.269 - 0.336: 3 Chirality restraints: 4657 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4654 not shown) Planarity restraints: 5112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 40 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C PHE E 40 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE E 40 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR E 41 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 902 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C MET A 902 " 0.049 2.00e-02 2.50e+03 pdb=" O MET A 902 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO E 590 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.039 5.00e-02 4.00e+02 ... (remaining 5109 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7470 2.80 - 3.33: 24659 3.33 - 3.85: 49250 3.85 - 4.38: 56435 4.38 - 4.90: 96949 Nonbonded interactions: 234763 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.294 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.311 3.040 ... (remaining 234758 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.120 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.005 0.064 29345 Z= 0.240 Angle : 0.854 14.834 40063 Z= 0.455 Chirality : 0.057 0.336 4657 Planarity : 0.006 0.068 5066 Dihedral : 12.959 89.731 11520 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 3465 helix: 0.87 (0.15), residues: 992 sheet: 0.57 (0.18), residues: 700 loop : -0.79 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 460 TYR 0.046 0.002 TYR A 200 PHE 0.033 0.002 PHE C 238 TRP 0.026 0.002 TRP E 69 HIS 0.006 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00487 (29241) covalent geometry : angle 0.82118 (39791) SS BOND : bond 0.00333 ( 40) SS BOND : angle 1.54774 ( 80) hydrogen bonds : bond 0.12503 ( 1139) hydrogen bonds : angle 6.74011 ( 3204) link_BETA1-4 : bond 0.00539 ( 18) link_BETA1-4 : angle 1.71430 ( 54) link_NAG-ASN : bond 0.00723 ( 46) link_NAG-ASN : angle 3.86888 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.998 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 1029 MET cc_start: 0.9200 (tpp) cc_final: 0.8974 (tpp) REVERT: C 351 TYR cc_start: 0.8233 (p90) cc_final: 0.7650 (p90) REVERT: C 374 PHE cc_start: 0.7303 (m-80) cc_final: 0.7047 (m-80) REVERT: C 421 TYR cc_start: 0.7677 (m-10) cc_final: 0.6868 (m-80) REVERT: C 571 ASP cc_start: 0.7887 (m-30) cc_final: 0.7213 (p0) REVERT: E 408 MET cc_start: 0.8264 (mmt) cc_final: 0.8017 (mpm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.7700 time to fit residues: 167.3777 Evaluate side-chains 88 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A1011 GLN B 115 GLN B 493 GLN B1002 GLN C 613 GLN C 901 GLN E 374 HIS E 472 GLN E 552 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.085742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.051611 restraints weight = 128073.443| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.85 r_work: 0.3031 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29345 Z= 0.142 Angle : 0.575 11.223 40063 Z= 0.286 Chirality : 0.044 0.359 4657 Planarity : 0.004 0.054 5066 Dihedral : 5.623 54.812 5105 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.68 % Allowed : 6.45 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3465 helix: 1.85 (0.16), residues: 1021 sheet: 0.64 (0.19), residues: 685 loop : -0.58 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.015 0.001 TYR B 495 PHE 0.025 0.001 PHE C 342 TRP 0.014 0.001 TRP E 165 HIS 0.003 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00311 (29241) covalent geometry : angle 0.54832 (39791) SS BOND : bond 0.00270 ( 40) SS BOND : angle 1.00675 ( 80) hydrogen bonds : bond 0.04193 ( 1139) hydrogen bonds : angle 5.43748 ( 3204) link_BETA1-4 : bond 0.00273 ( 18) link_BETA1-4 : angle 0.98871 ( 54) link_NAG-ASN : bond 0.00517 ( 46) link_NAG-ASN : angle 2.88214 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9554 (tpp) cc_final: 0.9327 (tpp) REVERT: B 198 ASP cc_start: 0.8836 (m-30) cc_final: 0.8622 (t0) REVERT: C 351 TYR cc_start: 0.8320 (p90) cc_final: 0.8088 (p90) REVERT: C 421 TYR cc_start: 0.7964 (m-10) cc_final: 0.7734 (m-80) REVERT: C 508 TYR cc_start: 0.8946 (m-80) cc_final: 0.8735 (m-80) REVERT: C 571 ASP cc_start: 0.8504 (m-30) cc_final: 0.7552 (p0) REVERT: E 249 MET cc_start: 0.0782 (mtt) cc_final: 0.0522 (mmm) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 0.6749 time to fit residues: 89.9987 Evaluate side-chains 90 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 186 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 564 GLN B 613 GLN C 580 GLN C 762 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.084573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.050300 restraints weight = 127818.673| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.70 r_work: 0.2983 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29345 Z= 0.170 Angle : 0.556 13.267 40063 Z= 0.274 Chirality : 0.043 0.302 4657 Planarity : 0.004 0.043 5066 Dihedral : 5.124 55.895 5105 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.17 % Allowed : 7.03 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3465 helix: 2.12 (0.16), residues: 1020 sheet: 0.56 (0.19), residues: 682 loop : -0.43 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 214 TYR 0.018 0.001 TYR B1067 PHE 0.022 0.001 PHE C 342 TRP 0.020 0.002 TRP A 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00379 (29241) covalent geometry : angle 0.53344 (39791) SS BOND : bond 0.00197 ( 40) SS BOND : angle 0.90882 ( 80) hydrogen bonds : bond 0.04043 ( 1139) hydrogen bonds : angle 5.14849 ( 3204) link_BETA1-4 : bond 0.00257 ( 18) link_BETA1-4 : angle 1.02542 ( 54) link_NAG-ASN : bond 0.00545 ( 46) link_NAG-ASN : angle 2.62129 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9452 (tpt) cc_final: 0.9202 (tpp) REVERT: B 198 ASP cc_start: 0.8921 (m-30) cc_final: 0.8657 (t0) REVERT: C 153 MET cc_start: 0.4924 (pp-130) cc_final: 0.4584 (tmm) REVERT: C 351 TYR cc_start: 0.8365 (p90) cc_final: 0.8058 (p90) REVERT: C 508 TYR cc_start: 0.8957 (m-80) cc_final: 0.8715 (m-10) REVERT: C 571 ASP cc_start: 0.8389 (m-30) cc_final: 0.7482 (p0) REVERT: E 249 MET cc_start: 0.1053 (mtt) cc_final: 0.0756 (mmm) outliers start: 36 outliers final: 9 residues processed: 111 average time/residue: 0.5466 time to fit residues: 73.9932 Evaluate side-chains 84 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 201 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 302 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** E 535 HIS ** 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 = 0.4128 r_free = 0.4128 target = 0.084486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.050531 restraints weight = 127819.449| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.69 r_work: 0.2986 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29345 Z= 0.128 Angle : 0.512 10.325 40063 Z= 0.252 Chirality : 0.043 0.290 4657 Planarity : 0.003 0.038 5066 Dihedral : 4.828 56.010 5105 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.97 % Allowed : 8.03 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3465 helix: 2.22 (0.16), residues: 1032 sheet: 0.38 (0.20), residues: 631 loop : -0.27 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.015 0.001 TYR A1067 PHE 0.020 0.001 PHE C 342 TRP 0.023 0.001 TRP A 104 HIS 0.003 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00281 (29241) covalent geometry : angle 0.49037 (39791) SS BOND : bond 0.00168 ( 40) SS BOND : angle 0.76220 ( 80) hydrogen bonds : bond 0.03710 ( 1139) hydrogen bonds : angle 4.93886 ( 3204) link_BETA1-4 : bond 0.00328 ( 18) link_BETA1-4 : angle 0.96005 ( 54) link_NAG-ASN : bond 0.00481 ( 46) link_NAG-ASN : angle 2.46009 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9426 (tpt) cc_final: 0.9191 (tpp) REVERT: A 1029 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9108 (tpp) REVERT: B 198 ASP cc_start: 0.8931 (m-30) cc_final: 0.8670 (t0) REVERT: C 153 MET cc_start: 0.4579 (pp-130) cc_final: 0.4318 (tmm) REVERT: C 351 TYR cc_start: 0.8367 (p90) cc_final: 0.8135 (p90) REVERT: C 508 TYR cc_start: 0.8897 (m-80) cc_final: 0.8640 (m-10) REVERT: C 571 ASP cc_start: 0.8409 (m-30) cc_final: 0.7596 (p0) REVERT: E 249 MET cc_start: 0.1034 (mtt) cc_final: 0.0812 (mmm) REVERT: E 323 MET cc_start: 0.5333 (mmm) cc_final: 0.4955 (mtp) outliers start: 30 outliers final: 13 residues processed: 101 average time/residue: 0.6405 time to fit residues: 77.3105 Evaluate side-chains 89 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 20 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 824 ASN B 125 ASN B 824 ASN B 957 GLN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** E 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.082444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048045 restraints weight = 128397.393| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.75 r_work: 0.2910 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29345 Z= 0.286 Angle : 0.630 10.287 40063 Z= 0.309 Chirality : 0.045 0.260 4657 Planarity : 0.004 0.038 5066 Dihedral : 5.254 59.552 5105 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.52 % Allowed : 8.65 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3465 helix: 2.03 (0.16), residues: 1043 sheet: 0.04 (0.20), residues: 631 loop : -0.33 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 214 TYR 0.019 0.002 TYR C 269 PHE 0.021 0.002 PHE C 342 TRP 0.026 0.002 TRP A 104 HIS 0.005 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00642 (29241) covalent geometry : angle 0.60939 (39791) SS BOND : bond 0.00256 ( 40) SS BOND : angle 0.83169 ( 80) hydrogen bonds : bond 0.04328 ( 1139) hydrogen bonds : angle 5.21372 ( 3204) link_BETA1-4 : bond 0.00209 ( 18) link_BETA1-4 : angle 1.32021 ( 54) link_NAG-ASN : bond 0.00650 ( 46) link_NAG-ASN : angle 2.63093 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.8951 (m-30) cc_final: 0.8704 (t0) REVERT: C 351 TYR cc_start: 0.8291 (p90) cc_final: 0.7963 (p90) REVERT: C 508 TYR cc_start: 0.8790 (m-80) cc_final: 0.8502 (m-10) REVERT: C 571 ASP cc_start: 0.8660 (m-30) cc_final: 0.7868 (p0) outliers start: 47 outliers final: 14 residues processed: 112 average time/residue: 0.5952 time to fit residues: 80.8014 Evaluate side-chains 88 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 321 optimal weight: 20.0000 chunk 349 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 304 optimal weight: 20.0000 chunk 211 optimal weight: 0.0570 chunk 229 optimal weight: 9.9990 chunk 276 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 2.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 218 GLN E 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.082481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048577 restraints weight = 128053.965| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.48 r_work: 0.2936 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29345 Z= 0.217 Angle : 0.567 11.434 40063 Z= 0.279 Chirality : 0.044 0.276 4657 Planarity : 0.004 0.036 5066 Dihedral : 5.179 57.423 5105 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.13 % Allowed : 9.17 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3465 helix: 2.12 (0.16), residues: 1044 sheet: -0.16 (0.20), residues: 606 loop : -0.32 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.017 0.001 TYR B1067 PHE 0.022 0.001 PHE C 342 TRP 0.025 0.001 TRP A 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00486 (29241) covalent geometry : angle 0.54753 (39791) SS BOND : bond 0.00204 ( 40) SS BOND : angle 0.70598 ( 80) hydrogen bonds : bond 0.03937 ( 1139) hydrogen bonds : angle 5.04532 ( 3204) link_BETA1-4 : bond 0.00227 ( 18) link_BETA1-4 : angle 1.03259 ( 54) link_NAG-ASN : bond 0.00507 ( 46) link_NAG-ASN : angle 2.49472 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.9171 (tpp) REVERT: B 198 ASP cc_start: 0.8979 (m-30) cc_final: 0.8722 (t0) REVERT: C 153 MET cc_start: 0.4497 (tmm) cc_final: 0.4295 (tmm) REVERT: C 351 TYR cc_start: 0.8342 (p90) cc_final: 0.8050 (p90) REVERT: C 508 TYR cc_start: 0.8738 (m-80) cc_final: 0.8429 (m-10) outliers start: 35 outliers final: 16 residues processed: 102 average time/residue: 0.6255 time to fit residues: 76.3445 Evaluate side-chains 89 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 98 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 163 optimal weight: 0.5980 chunk 344 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN B 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.083036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.049415 restraints weight = 127511.115| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.53 r_work: 0.2956 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29345 Z= 0.126 Angle : 0.524 11.149 40063 Z= 0.257 Chirality : 0.043 0.280 4657 Planarity : 0.003 0.039 5066 Dihedral : 4.928 57.596 5105 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.91 % Allowed : 9.62 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3465 helix: 2.20 (0.16), residues: 1038 sheet: -0.11 (0.21), residues: 595 loop : -0.26 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.015 0.001 TYR A1067 PHE 0.021 0.001 PHE C 342 TRP 0.026 0.001 TRP A 104 HIS 0.003 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00279 (29241) covalent geometry : angle 0.50523 (39791) SS BOND : bond 0.00145 ( 40) SS BOND : angle 0.62729 ( 80) hydrogen bonds : bond 0.03707 ( 1139) hydrogen bonds : angle 4.90439 ( 3204) link_BETA1-4 : bond 0.00240 ( 18) link_BETA1-4 : angle 1.00084 ( 54) link_NAG-ASN : bond 0.00471 ( 46) link_NAG-ASN : angle 2.36853 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9056 (m-30) cc_final: 0.8807 (t0) REVERT: C 351 TYR cc_start: 0.8304 (p90) cc_final: 0.8039 (p90) REVERT: C 508 TYR cc_start: 0.8675 (m-80) cc_final: 0.8366 (m-10) outliers start: 28 outliers final: 15 residues processed: 97 average time/residue: 0.7114 time to fit residues: 81.6703 Evaluate side-chains 87 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 255 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 343 optimal weight: 0.0020 chunk 154 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 246 optimal weight: 7.9990 chunk 275 optimal weight: 0.0050 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.083321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.050125 restraints weight = 128975.317| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.56 r_work: 0.2972 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29345 Z= 0.102 Angle : 0.518 11.671 40063 Z= 0.253 Chirality : 0.043 0.284 4657 Planarity : 0.003 0.040 5066 Dihedral : 4.745 57.565 5105 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.07 % Allowed : 9.69 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3465 helix: 2.17 (0.16), residues: 1049 sheet: -0.10 (0.21), residues: 593 loop : -0.19 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.013 0.001 TYR A1067 PHE 0.020 0.001 PHE C 342 TRP 0.031 0.001 TRP A 104 HIS 0.003 0.000 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00223 (29241) covalent geometry : angle 0.50034 (39791) SS BOND : bond 0.00125 ( 40) SS BOND : angle 0.60118 ( 80) hydrogen bonds : bond 0.03571 ( 1139) hydrogen bonds : angle 4.80933 ( 3204) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 0.94077 ( 54) link_NAG-ASN : bond 0.00455 ( 46) link_NAG-ASN : angle 2.28305 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9007 (m-30) cc_final: 0.8742 (t0) REVERT: C 47 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9274 (m) REVERT: C 351 TYR cc_start: 0.8270 (p90) cc_final: 0.7971 (p90) REVERT: C 508 TYR cc_start: 0.8678 (m-80) cc_final: 0.8356 (m-10) REVERT: C 571 ASP cc_start: 0.8544 (m-30) cc_final: 0.7798 (p0) outliers start: 33 outliers final: 14 residues processed: 96 average time/residue: 0.6625 time to fit residues: 75.3037 Evaluate side-chains 86 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 105 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 316 optimal weight: 30.0000 chunk 234 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 272 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 613 GLN B 125 ASN C 824 ASN E 250 ASN ** E 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.081657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047567 restraints weight = 127771.903| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.53 r_work: 0.2910 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 29345 Z= 0.305 Angle : 0.634 13.008 40063 Z= 0.311 Chirality : 0.045 0.261 4657 Planarity : 0.004 0.037 5066 Dihedral : 5.212 59.954 5105 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.81 % Allowed : 9.98 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3465 helix: 1.93 (0.16), residues: 1053 sheet: -0.24 (0.20), residues: 663 loop : -0.32 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.019 0.002 TYR B1067 PHE 0.022 0.002 PHE C 238 TRP 0.024 0.002 TRP A 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00683 (29241) covalent geometry : angle 0.61483 (39791) SS BOND : bond 0.00257 ( 40) SS BOND : angle 0.74828 ( 80) hydrogen bonds : bond 0.04256 ( 1139) hydrogen bonds : angle 5.14484 ( 3204) link_BETA1-4 : bond 0.00193 ( 18) link_BETA1-4 : angle 1.31715 ( 54) link_NAG-ASN : bond 0.00616 ( 46) link_NAG-ASN : angle 2.55890 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3805 (tmm) cc_final: 0.3542 (ppp) REVERT: B 198 ASP cc_start: 0.9147 (m-30) cc_final: 0.8809 (t0) REVERT: C 351 TYR cc_start: 0.8279 (p90) cc_final: 0.8025 (p90) REVERT: C 508 TYR cc_start: 0.8640 (m-80) cc_final: 0.8330 (m-10) outliers start: 25 outliers final: 15 residues processed: 91 average time/residue: 0.6759 time to fit residues: 73.0814 Evaluate side-chains 87 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 117 optimal weight: 8.9990 chunk 253 optimal weight: 0.7980 chunk 218 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 321 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN C 121 ASN ** E 522 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 = 0.4072 r_free = 0.4072 target = 0.081982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.048074 restraints weight = 127014.225| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.48 r_work: 0.2926 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29345 Z= 0.214 Angle : 0.581 13.054 40063 Z= 0.285 Chirality : 0.044 0.276 4657 Planarity : 0.004 0.039 5066 Dihedral : 5.188 58.429 5105 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.68 % Allowed : 10.14 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3465 helix: 1.99 (0.16), residues: 1055 sheet: -0.32 (0.21), residues: 622 loop : -0.27 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.017 0.001 TYR C1067 PHE 0.022 0.001 PHE C 342 TRP 0.034 0.002 TRP A 104 HIS 0.003 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00481 (29241) covalent geometry : angle 0.56257 (39791) SS BOND : bond 0.00185 ( 40) SS BOND : angle 0.67562 ( 80) hydrogen bonds : bond 0.03938 ( 1139) hydrogen bonds : angle 5.04786 ( 3204) link_BETA1-4 : bond 0.00206 ( 18) link_BETA1-4 : angle 1.09043 ( 54) link_NAG-ASN : bond 0.00501 ( 46) link_NAG-ASN : angle 2.46472 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9205 (m-30) cc_final: 0.8872 (t0) REVERT: C 47 VAL cc_start: 0.9467 (OUTLIER) cc_final: 0.9196 (m) REVERT: C 351 TYR cc_start: 0.8276 (p90) cc_final: 0.8027 (p90) REVERT: C 508 TYR cc_start: 0.8647 (m-80) cc_final: 0.8340 (m-10) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.7012 time to fit residues: 78.6294 Evaluate side-chains 90 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 123 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 125 ASN E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.082438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.049960 restraints weight = 128591.091| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.91 r_work: 0.2920 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29345 Z= 0.138 Angle : 0.552 13.490 40063 Z= 0.269 Chirality : 0.043 0.281 4657 Planarity : 0.003 0.037 5066 Dihedral : 4.954 58.102 5105 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.62 % Allowed : 10.27 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3465 helix: 2.13 (0.16), residues: 1046 sheet: -0.16 (0.21), residues: 602 loop : -0.20 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.021 0.001 TYR B 904 PHE 0.025 0.001 PHE C 238 TRP 0.034 0.001 TRP A 104 HIS 0.004 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00310 (29241) covalent geometry : angle 0.53417 (39791) SS BOND : bond 0.00143 ( 40) SS BOND : angle 0.62582 ( 80) hydrogen bonds : bond 0.03691 ( 1139) hydrogen bonds : angle 4.93292 ( 3204) link_BETA1-4 : bond 0.00248 ( 18) link_BETA1-4 : angle 1.02308 ( 54) link_NAG-ASN : bond 0.00445 ( 46) link_NAG-ASN : angle 2.34596 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13343.90 seconds wall clock time: 227 minutes 9.24 seconds (13629.24 seconds total)