Starting phenix.real_space_refine on Sat Mar 7 02:47:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgb_32482/03_2026/7wgb_32482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgb_32482/03_2026/7wgb_32482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wgb_32482/03_2026/7wgb_32482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgb_32482/03_2026/7wgb_32482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wgb_32482/03_2026/7wgb_32482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgb_32482/03_2026/7wgb_32482.map" } resolution = 3.5 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= 0.074 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 175 5.16 5 C 23421 2.51 5 N 6003 2.21 5 O 7120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36719 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "D" Number of atoms: 4852 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} bond proxies already assigned to first conformer: 4972 Chain: "F" Number of atoms: 4852 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} bond proxies already assigned to first conformer: 4972 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.32, per 1000 atoms: 0.28 Number of scatterers: 36719 At special positions: 0 Unit cell: (138.03, 163.71, 263.22, 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 175 16.00 O 7120 8.00 N 6003 7.00 C 23421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 163 " 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 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=6, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 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 K 2 " - " BMA K 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A1303 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 145 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 53 " " NAG F 701 " - " ASN F 546 " " NAG F 702 " - " ASN F 90 " " NAG F 703 " - " ASN F 322 " " NAG F 704 " - " ASN F 53 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 331 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " NAG-SER " NAG C1302 " - " SER C 254 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8450 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 43 sheets defined 36.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.681A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.997A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.614A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.588A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.704A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.352A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.641A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.618A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 4.216A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.149A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.750A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.775A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.177A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.946A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.398A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.346A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.137A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.574A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.342A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.666A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.587A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.056A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 882 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.522A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 4.151A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.757A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.029A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.764A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.945A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.639A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.759A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.824A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.337A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.669A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.795A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.599A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) 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: 3.712A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (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 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.898A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.058A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.529A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.566A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.082A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.231A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.592A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.699A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 158 through 169 removed outlier: 4.178A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.720A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 252 removed outlier: 4.333A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 277 through 283 removed outlier: 4.024A pdb=" N VAL D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.999A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.534A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.179A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.718A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 471 through 474 removed outlier: 3.841A pdb=" N MET D 474 " --> pdb=" O ASP D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.914A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.687A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 558 Processing helix chain 'D' and resid 565 through 574 removed outlier: 4.130A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 4.605A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.952A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.503A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.778A pdb=" N SER F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.713A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 173 removed outlier: 4.329A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 218 through 250 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.592A pdb=" N LEU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.724A pdb=" N MET F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 325 through 330 removed outlier: 4.181A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.876A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 4.072A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.623A pdb=" N LEU F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 472 through 485 removed outlier: 3.861A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.555A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 531 Processing helix chain 'F' and resid 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 547 through 561 removed outlier: 4.001A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 560 " --> pdb=" O ASN F 556 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY F 561 " --> pdb=" O MET F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.984A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 203 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 229 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER A 205 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.711A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.762A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.622A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.587A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.392A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.913A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.689A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.787A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.251A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N VAL B 126 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLU B 166 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE B 128 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR B 164 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 130 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN B 162 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B 132 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 160 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN B 134 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 318 removed outlier: 4.551A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.581A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.607A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.904A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 551 through 554 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.800A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 656 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.536A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.678A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AC8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.724A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE C 201 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP C 230 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 203 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 226 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.647A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD3, first strand: chain 'C' and resid 116 through 122 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.883A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD6, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.509A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.741A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.621A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.899A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.585A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (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 'C' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.735A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.320A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 347 through 349 1480 hydrogen bonds defined for protein. 4153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.14 Time building geometry restraints manager: 3.89 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: 11588 1.34 - 1.46: 9491 1.46 - 1.59: 16284 1.59 - 1.71: 0 1.71 - 1.84: 247 Bond restraints: 37610 Sorted by residual: bond pdb=" N ASN B 145 " pdb=" CA ASN B 145 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" C ASP B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.19e-02 7.06e+03 6.83e+00 bond pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.44e+00 bond pdb=" N SER B 148 " pdb=" CA SER B 148 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.37e+00 ... (remaining 37605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 50335 2.29 - 4.58: 721 4.58 - 6.88: 69 6.88 - 9.17: 12 9.17 - 11.46: 1 Bond angle restraints: 51138 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.14 117.60 -6.46 1.46e+00 4.69e-01 1.96e+01 angle pdb=" CA LYS B 144 " pdb=" C LYS B 144 " pdb=" O LYS B 144 " ideal model delta sigma weight residual 122.31 116.70 5.61 1.31e+00 5.83e-01 1.84e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 109.42 4.11 9.80e-01 1.04e+00 1.76e+01 angle pdb=" N HIS B 143 " pdb=" CA HIS B 143 " pdb=" C HIS B 143 " ideal model delta sigma weight residual 108.41 114.80 -6.39 1.61e+00 3.86e-01 1.58e+01 angle pdb=" N LEU B 141 " pdb=" CA LEU B 141 " pdb=" C LEU B 141 " ideal model delta sigma weight residual 113.38 108.61 4.77 1.23e+00 6.61e-01 1.50e+01 ... (remaining 51133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 21499 22.06 - 44.12: 1663 44.12 - 66.18: 175 66.18 - 88.24: 70 88.24 - 110.29: 26 Dihedral angle restraints: 23433 sinusoidal: 10316 harmonic: 13117 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 -177.99 -89.01 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.66 84.34 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 165.66 -72.66 1 1.00e+01 1.00e-02 6.74e+01 ... (remaining 23430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5212 0.075 - 0.149: 631 0.149 - 0.224: 20 0.224 - 0.298: 11 0.298 - 0.373: 3 Chirality restraints: 5877 Sorted by residual: chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 5874 not shown) Planarity restraints: 6534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO C 330 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 83 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.47e+00 pdb=" N PRO D 84 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 84 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 84 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 214 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 215 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.039 5.00e-02 4.00e+02 ... (remaining 6531 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 925 2.68 - 3.24: 37003 3.24 - 3.79: 56762 3.79 - 4.35: 72179 4.35 - 4.90: 117190 Nonbonded interactions: 284059 Sorted by model distance: nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR D 55 " pdb=" OD1 ASN D 58 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 489 " pdb=" OH TYR F 83 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR C 581 " pdb=" OE1 GLU C 583 " model vdw 2.166 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 3.040 ... (remaining 284054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1308) selection = (chain 'C' and resid 14 through 1308) } ncs_group { reference = (chain 'D' and (resid 19 through 227 or resid 229 through 704)) selection = (chain 'F' and (resid 19 through 227 or resid 229 through 704)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.710 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37728 Z= 0.190 Angle : 0.667 11.460 51428 Z= 0.334 Chirality : 0.047 0.373 5877 Planarity : 0.004 0.076 6494 Dihedral : 15.286 110.294 14848 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4450 helix: 0.82 (0.14), residues: 1423 sheet: 0.22 (0.21), residues: 606 loop : -1.87 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.032 0.001 TYR D 199 PHE 0.030 0.001 PHE F 452 TRP 0.024 0.001 TRP F 566 HIS 0.006 0.001 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.00394 (37610) covalent geometry : angle 0.65433 (51138) SS BOND : bond 0.00337 ( 45) SS BOND : angle 1.26895 ( 90) hydrogen bonds : bond 0.12965 ( 1480) hydrogen bonds : angle 6.09980 ( 4153) Misc. bond : bond 0.00081 ( 6) link_BETA1-4 : bond 0.00501 ( 26) link_BETA1-4 : angle 1.72439 ( 78) link_NAG-ASN : bond 0.00388 ( 40) link_NAG-ASN : angle 2.30707 ( 120) link_NAG-SER : bond 0.00009 ( 1) link_NAG-SER : angle 1.19007 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1017 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 759 PHE cc_start: 0.7236 (t80) cc_final: 0.6891 (t80) REVERT: D 69 TRP cc_start: 0.2001 (t-100) cc_final: 0.0958 (t60) REVERT: D 249 MET cc_start: 0.3632 (mtt) cc_final: 0.3430 (mmt) REVERT: F 498 CYS cc_start: 0.6572 (t) cc_final: 0.6250 (t) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1910 time to fit residues: 55.5477 Evaluate side-chains 126 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 30.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1159 HIS B 134 GLN C 220 GLN C 370 ASN C 955 ASN C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.119111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085248 restraints weight = 169044.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086036 restraints weight = 83983.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085845 restraints weight = 57373.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086152 restraints weight = 57262.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086366 restraints weight = 47646.557| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37728 Z= 0.193 Angle : 0.643 10.236 51428 Z= 0.325 Chirality : 0.045 0.408 5877 Planarity : 0.005 0.075 6494 Dihedral : 8.958 77.570 6508 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 0.38 % Allowed : 7.58 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.97 (0.12), residues: 4450 helix: 0.80 (0.14), residues: 1424 sheet: 0.25 (0.21), residues: 611 loop : -1.87 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 169 TYR 0.022 0.001 TYR D 385 PHE 0.031 0.002 PHE D 369 TRP 0.045 0.002 TRP D 203 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00441 (37610) covalent geometry : angle 0.62865 (51138) SS BOND : bond 0.00557 ( 45) SS BOND : angle 1.24124 ( 90) hydrogen bonds : bond 0.05054 ( 1480) hydrogen bonds : angle 5.33496 ( 4153) Misc. bond : bond 0.00050 ( 6) link_BETA1-4 : bond 0.00497 ( 26) link_BETA1-4 : angle 1.82088 ( 78) link_NAG-ASN : bond 0.00473 ( 40) link_NAG-ASN : angle 2.27763 ( 120) link_NAG-SER : bond 0.00259 ( 1) link_NAG-SER : angle 1.22036 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.7276 (mpp) cc_final: 0.7027 (mpp) REVERT: D 249 MET cc_start: 0.2900 (mtt) cc_final: 0.2487 (mtt) REVERT: F 270 MET cc_start: 0.5025 (mpp) cc_final: 0.4753 (mpp) REVERT: F 498 CYS cc_start: 0.6355 (t) cc_final: 0.6099 (t) outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 0.1938 time to fit residues: 49.6691 Evaluate side-chains 131 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 144 optimal weight: 4.9990 chunk 129 optimal weight: 40.0000 chunk 150 optimal weight: 10.0000 chunk 176 optimal weight: 0.6980 chunk 437 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 413 optimal weight: 6.9990 chunk 363 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 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 = 0.4263 r_free = 0.4263 target = 0.118387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083892 restraints weight = 186811.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085316 restraints weight = 84035.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084988 restraints weight = 53647.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085318 restraints weight = 50730.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085530 restraints weight = 44129.849| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 37728 Z= 0.203 Angle : 0.642 10.342 51428 Z= 0.325 Chirality : 0.045 0.404 5877 Planarity : 0.005 0.075 6494 Dihedral : 7.660 59.385 6508 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.72 % Rotamer: Outliers : 0.91 % Allowed : 11.28 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 4450 helix: 0.76 (0.14), residues: 1420 sheet: 0.16 (0.21), residues: 610 loop : -1.90 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.021 0.001 TYR D 385 PHE 0.032 0.001 PHE D 369 TRP 0.053 0.002 TRP D 203 HIS 0.011 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00467 (37610) covalent geometry : angle 0.62809 (51138) SS BOND : bond 0.00314 ( 45) SS BOND : angle 1.18143 ( 90) hydrogen bonds : bond 0.04938 ( 1480) hydrogen bonds : angle 5.28758 ( 4153) Misc. bond : bond 0.00043 ( 6) link_BETA1-4 : bond 0.00469 ( 26) link_BETA1-4 : angle 1.81954 ( 78) link_NAG-ASN : bond 0.00508 ( 40) link_NAG-ASN : angle 2.29331 ( 120) link_NAG-SER : bond 0.00098 ( 1) link_NAG-SER : angle 1.60843 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5371 (m-10) cc_final: 0.5082 (m-80) REVERT: D 249 MET cc_start: 0.2753 (mtt) cc_final: 0.2281 (mtt) REVERT: F 249 MET cc_start: -0.2672 (tpp) cc_final: -0.2884 (mmp) REVERT: F 270 MET cc_start: 0.5097 (mpp) cc_final: 0.4671 (mpp) REVERT: F 498 CYS cc_start: 0.6455 (t) cc_final: 0.6168 (t) REVERT: F 579 MET cc_start: -0.0067 (ttt) cc_final: -0.0917 (mpp) outliers start: 35 outliers final: 17 residues processed: 165 average time/residue: 0.1920 time to fit residues: 56.5814 Evaluate side-chains 146 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 360 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 378 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 405 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 127 optimal weight: 0.0000 chunk 55 optimal weight: 7.9990 overall best weight: 2.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.118910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084171 restraints weight = 223797.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085340 restraints weight = 110968.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085846 restraints weight = 59100.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.086162 restraints weight = 48172.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.086303 restraints weight = 41074.615| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37728 Z= 0.165 Angle : 0.608 10.414 51428 Z= 0.307 Chirality : 0.044 0.396 5877 Planarity : 0.004 0.074 6494 Dihedral : 6.869 59.897 6508 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer: Outliers : 1.17 % Allowed : 13.36 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -0.97 (0.12), residues: 4450 helix: 0.83 (0.14), residues: 1421 sheet: 0.15 (0.21), residues: 618 loop : -1.87 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.020 0.001 TYR D 385 PHE 0.030 0.001 PHE D 369 TRP 0.053 0.002 TRP D 203 HIS 0.007 0.001 HIS A1159 Details of bonding type rmsd covalent geometry : bond 0.00377 (37610) covalent geometry : angle 0.59325 (51138) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.31466 ( 90) hydrogen bonds : bond 0.04603 ( 1480) hydrogen bonds : angle 5.15207 ( 4153) Misc. bond : bond 0.00047 ( 6) link_BETA1-4 : bond 0.00433 ( 26) link_BETA1-4 : angle 1.77483 ( 78) link_NAG-ASN : bond 0.00436 ( 40) link_NAG-ASN : angle 2.20356 ( 120) link_NAG-SER : bond 0.00096 ( 1) link_NAG-SER : angle 1.20809 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5350 (m-10) cc_final: 0.5064 (m-80) REVERT: A 1010 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: C 303 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8263 (tt) REVERT: D 249 MET cc_start: 0.2631 (mtt) cc_final: 0.2120 (mtt) REVERT: F 270 MET cc_start: 0.5161 (mpp) cc_final: 0.4628 (mpp) REVERT: F 376 MET cc_start: 0.3336 (ptp) cc_final: 0.3106 (ptp) REVERT: F 473 TRP cc_start: 0.3123 (m-90) cc_final: 0.2617 (m-90) REVERT: F 498 CYS cc_start: 0.6579 (t) cc_final: 0.6369 (t) outliers start: 45 outliers final: 24 residues processed: 181 average time/residue: 0.1913 time to fit residues: 61.3815 Evaluate side-chains 154 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 61 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 340 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 208 optimal weight: 0.0570 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.4281 r_free = 0.4281 target = 0.119048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.085115 restraints weight = 171889.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085501 restraints weight = 89839.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085819 restraints weight = 59815.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085998 restraints weight = 50850.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086142 restraints weight = 45204.632| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37728 Z= 0.124 Angle : 0.584 15.991 51428 Z= 0.292 Chirality : 0.043 0.388 5877 Planarity : 0.004 0.074 6494 Dihedral : 6.288 58.835 6508 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 1.24 % Allowed : 14.55 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -0.83 (0.13), residues: 4450 helix: 0.98 (0.14), residues: 1428 sheet: 0.19 (0.21), residues: 617 loop : -1.79 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 634 TYR 0.020 0.001 TYR D 385 PHE 0.027 0.001 PHE D 369 TRP 0.071 0.001 TRP F 477 HIS 0.020 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00279 (37610) covalent geometry : angle 0.57104 (51138) SS BOND : bond 0.00358 ( 45) SS BOND : angle 1.16404 ( 90) hydrogen bonds : bond 0.04253 ( 1480) hydrogen bonds : angle 4.98807 ( 4153) Misc. bond : bond 0.00045 ( 6) link_BETA1-4 : bond 0.00464 ( 26) link_BETA1-4 : angle 1.68277 ( 78) link_NAG-ASN : bond 0.00386 ( 40) link_NAG-ASN : angle 2.11587 ( 120) link_NAG-SER : bond 0.00009 ( 1) link_NAG-SER : angle 0.70449 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5456 (m-10) cc_final: 0.5142 (m-80) REVERT: A 271 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: A 1010 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8414 (mp10) REVERT: B 633 TRP cc_start: 0.7205 (p90) cc_final: 0.6898 (p90) REVERT: B 740 MET cc_start: 0.8645 (mtp) cc_final: 0.8303 (mtp) REVERT: C 773 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 867 ASP cc_start: 0.7919 (p0) cc_final: 0.7693 (p0) REVERT: D 69 TRP cc_start: 0.1482 (t-100) cc_final: -0.0083 (t60) REVERT: D 249 MET cc_start: 0.2667 (mtt) cc_final: 0.2297 (mmt) REVERT: D 579 MET cc_start: 0.0293 (mpp) cc_final: -0.0985 (mtm) REVERT: F 473 TRP cc_start: 0.3232 (m-90) cc_final: 0.2721 (m-90) REVERT: F 498 CYS cc_start: 0.6407 (t) cc_final: 0.6170 (t) outliers start: 48 outliers final: 28 residues processed: 187 average time/residue: 0.1856 time to fit residues: 61.1118 Evaluate side-chains 161 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 275 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 427 optimal weight: 20.0000 chunk 383 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.116374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.082413 restraints weight = 165824.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083459 restraints weight = 82423.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082950 restraints weight = 58369.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083303 restraints weight = 59624.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.083477 restraints weight = 50107.955| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 37728 Z= 0.355 Angle : 0.784 15.766 51428 Z= 0.394 Chirality : 0.048 0.431 5877 Planarity : 0.005 0.075 6494 Dihedral : 7.131 54.469 6508 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.40 % Favored : 90.49 % Rotamer: Outliers : 2.10 % Allowed : 15.85 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.12), residues: 4450 helix: 0.52 (0.14), residues: 1427 sheet: -0.11 (0.21), residues: 606 loop : -2.07 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 634 TYR 0.022 0.002 TYR A 170 PHE 0.041 0.002 PHE D 369 TRP 0.058 0.002 TRP F 477 HIS 0.008 0.002 HIS A1159 Details of bonding type rmsd covalent geometry : bond 0.00820 (37610) covalent geometry : angle 0.76973 (51138) SS BOND : bond 0.00445 ( 45) SS BOND : angle 1.57698 ( 90) hydrogen bonds : bond 0.05536 ( 1480) hydrogen bonds : angle 5.58801 ( 4153) Misc. bond : bond 0.00055 ( 6) link_BETA1-4 : bond 0.00536 ( 26) link_BETA1-4 : angle 1.77145 ( 78) link_NAG-ASN : bond 0.00881 ( 40) link_NAG-ASN : angle 2.57049 ( 120) link_NAG-SER : bond 0.00316 ( 1) link_NAG-SER : angle 2.56368 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 131 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: A 186 PHE cc_start: 0.5687 (m-10) cc_final: 0.5325 (m-80) REVERT: A 271 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: A 1010 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8459 (mp10) REVERT: B 725 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 190 ARG cc_start: 0.7726 (mtp180) cc_final: 0.6543 (mmm160) REVERT: C 303 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (tt) REVERT: D 183 TYR cc_start: 0.0692 (OUTLIER) cc_final: 0.0406 (t80) REVERT: D 249 MET cc_start: 0.2569 (mtt) cc_final: 0.2062 (mtt) REVERT: F 270 MET cc_start: 0.5044 (mpp) cc_final: 0.4511 (mpp) REVERT: F 498 CYS cc_start: 0.6569 (t) cc_final: 0.6343 (t) outliers start: 82 outliers final: 53 residues processed: 208 average time/residue: 0.1884 time to fit residues: 70.0181 Evaluate side-chains 184 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 80 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 278 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 351 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 361 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.118137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.083137 restraints weight = 193330.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.085087 restraints weight = 84746.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085020 restraints weight = 49588.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.085475 restraints weight = 43758.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.085498 restraints weight = 39209.442| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37728 Z= 0.154 Angle : 0.628 14.833 51428 Z= 0.315 Chirality : 0.044 0.392 5877 Planarity : 0.004 0.072 6494 Dihedral : 6.538 56.193 6508 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.27 % Favored : 93.62 % Rotamer: Outliers : 1.62 % Allowed : 17.09 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4450 helix: 0.78 (0.14), residues: 1438 sheet: -0.06 (0.21), residues: 630 loop : -1.94 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 634 TYR 0.020 0.001 TYR D 385 PHE 0.031 0.001 PHE D 369 TRP 0.077 0.002 TRP F 477 HIS 0.007 0.001 HIS A1159 Details of bonding type rmsd covalent geometry : bond 0.00350 (37610) covalent geometry : angle 0.61421 (51138) SS BOND : bond 0.00385 ( 45) SS BOND : angle 1.25577 ( 90) hydrogen bonds : bond 0.04672 ( 1480) hydrogen bonds : angle 5.19091 ( 4153) Misc. bond : bond 0.00047 ( 6) link_BETA1-4 : bond 0.00434 ( 26) link_BETA1-4 : angle 1.67793 ( 78) link_NAG-ASN : bond 0.00427 ( 40) link_NAG-ASN : angle 2.24611 ( 120) link_NAG-SER : bond 0.00095 ( 1) link_NAG-SER : angle 1.15554 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: A 186 PHE cc_start: 0.5483 (m-10) cc_final: 0.5188 (m-80) REVERT: A 1010 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: B 725 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 190 ARG cc_start: 0.7545 (mtp180) cc_final: 0.6318 (mmm160) REVERT: C 303 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8304 (tt) REVERT: D 249 MET cc_start: 0.2982 (mtt) cc_final: 0.2553 (mmt) REVERT: F 270 MET cc_start: 0.5060 (mpp) cc_final: 0.4537 (mpp) REVERT: F 473 TRP cc_start: 0.3116 (m-90) cc_final: 0.2664 (m-90) outliers start: 63 outliers final: 45 residues processed: 193 average time/residue: 0.1933 time to fit residues: 66.2914 Evaluate side-chains 177 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 326 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 169 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 417 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 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 164 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.118686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084113 restraints weight = 224626.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.085295 restraints weight = 108252.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085633 restraints weight = 59865.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.085736 restraints weight = 60027.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086169 restraints weight = 46725.362| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37728 Z= 0.122 Angle : 0.605 13.887 51428 Z= 0.301 Chirality : 0.044 0.382 5877 Planarity : 0.004 0.072 6494 Dihedral : 6.095 56.151 6508 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 1.32 % Allowed : 17.62 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4450 helix: 0.96 (0.14), residues: 1424 sheet: 0.03 (0.21), residues: 637 loop : -1.85 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 634 TYR 0.020 0.001 TYR D 385 PHE 0.029 0.001 PHE F 464 TRP 0.076 0.001 TRP F 477 HIS 0.013 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00271 (37610) covalent geometry : angle 0.59160 (51138) SS BOND : bond 0.00301 ( 45) SS BOND : angle 1.21514 ( 90) hydrogen bonds : bond 0.04285 ( 1480) hydrogen bonds : angle 5.01503 ( 4153) Misc. bond : bond 0.00042 ( 6) link_BETA1-4 : bond 0.00479 ( 26) link_BETA1-4 : angle 1.63505 ( 78) link_NAG-ASN : bond 0.00395 ( 40) link_NAG-ASN : angle 2.20604 ( 120) link_NAG-SER : bond 0.00138 ( 1) link_NAG-SER : angle 0.89438 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: A 186 PHE cc_start: 0.5526 (m-10) cc_final: 0.5211 (m-80) REVERT: A 455 LEU cc_start: 0.6758 (mm) cc_final: 0.6517 (mp) REVERT: A 1010 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: B 423 TYR cc_start: 0.4762 (t80) cc_final: 0.4552 (t80) REVERT: B 633 TRP cc_start: 0.7264 (p90) cc_final: 0.6960 (p90) REVERT: B 725 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 190 ARG cc_start: 0.7523 (mtp180) cc_final: 0.6272 (mmm160) REVERT: C 303 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (tp) REVERT: C 370 ASN cc_start: 0.7245 (t0) cc_final: 0.6516 (p0) REVERT: C 773 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8062 (mt-10) REVERT: D 249 MET cc_start: 0.2934 (mtt) cc_final: 0.2532 (mmt) REVERT: F 270 MET cc_start: 0.5010 (mpp) cc_final: 0.4496 (mpp) REVERT: F 464 PHE cc_start: 0.2659 (OUTLIER) cc_final: 0.2365 (t80) REVERT: F 473 TRP cc_start: 0.3336 (m-90) cc_final: 0.2721 (m-90) outliers start: 51 outliers final: 36 residues processed: 184 average time/residue: 0.1845 time to fit residues: 60.2851 Evaluate side-chains 171 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 70 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 365 optimal weight: 40.0000 chunk 321 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 383 optimal weight: 9.9990 chunk 173 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.118086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.083490 restraints weight = 201958.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.084371 restraints weight = 92621.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085144 restraints weight = 58628.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085043 restraints weight = 41758.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085261 restraints weight = 43100.587| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37728 Z= 0.182 Angle : 0.638 13.686 51428 Z= 0.318 Chirality : 0.044 0.394 5877 Planarity : 0.004 0.072 6494 Dihedral : 6.160 55.363 6508 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.94 % Rotamer: Outliers : 1.42 % Allowed : 17.70 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4450 helix: 0.87 (0.14), residues: 1443 sheet: 0.15 (0.22), residues: 602 loop : -1.91 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 634 TYR 0.019 0.001 TYR D 385 PHE 0.031 0.001 PHE D 369 TRP 0.046 0.001 TRP D 203 HIS 0.015 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00418 (37610) covalent geometry : angle 0.62325 (51138) SS BOND : bond 0.00350 ( 45) SS BOND : angle 1.62530 ( 90) hydrogen bonds : bond 0.04509 ( 1480) hydrogen bonds : angle 5.12315 ( 4153) Misc. bond : bond 0.00040 ( 6) link_BETA1-4 : bond 0.00447 ( 26) link_BETA1-4 : angle 1.61758 ( 78) link_NAG-ASN : bond 0.00482 ( 40) link_NAG-ASN : angle 2.29331 ( 120) link_NAG-SER : bond 0.00098 ( 1) link_NAG-SER : angle 1.45022 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: A 186 PHE cc_start: 0.5433 (m-10) cc_final: 0.5216 (m-80) REVERT: A 1010 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: B 423 TYR cc_start: 0.4800 (t80) cc_final: 0.4582 (t80) REVERT: B 725 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 190 ARG cc_start: 0.7561 (mtp180) cc_final: 0.6318 (mmm160) REVERT: C 303 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8294 (tp) REVERT: C 370 ASN cc_start: 0.7191 (t0) cc_final: 0.6472 (p0) REVERT: C 773 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 249 MET cc_start: 0.2942 (mtt) cc_final: 0.2479 (mmt) REVERT: F 270 MET cc_start: 0.5074 (mpp) cc_final: 0.4545 (mpp) REVERT: F 464 PHE cc_start: 0.3013 (OUTLIER) cc_final: 0.2639 (t80) REVERT: F 473 TRP cc_start: 0.3304 (m-90) cc_final: 0.2710 (m-90) outliers start: 55 outliers final: 46 residues processed: 184 average time/residue: 0.1823 time to fit residues: 59.7621 Evaluate side-chains 182 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 179 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 442 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** 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 = 0.4280 r_free = 0.4280 target = 0.119033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.084515 restraints weight = 199561.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.085375 restraints weight = 90883.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086155 restraints weight = 54483.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.086152 restraints weight = 38726.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.086320 restraints weight = 40141.245| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37728 Z= 0.118 Angle : 0.601 13.168 51428 Z= 0.298 Chirality : 0.043 0.373 5877 Planarity : 0.004 0.071 6494 Dihedral : 5.793 56.138 6508 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.87 % Favored : 94.02 % Rotamer: Outliers : 1.29 % Allowed : 17.95 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.82 (0.13), residues: 4450 helix: 1.00 (0.14), residues: 1448 sheet: 0.12 (0.21), residues: 630 loop : -1.81 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 634 TYR 0.022 0.001 TYR D 385 PHE 0.026 0.001 PHE D 369 TRP 0.043 0.001 TRP D 203 HIS 0.014 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00264 (37610) covalent geometry : angle 0.58763 (51138) SS BOND : bond 0.00290 ( 45) SS BOND : angle 1.27812 ( 90) hydrogen bonds : bond 0.04125 ( 1480) hydrogen bonds : angle 4.93617 ( 4153) Misc. bond : bond 0.00044 ( 6) link_BETA1-4 : bond 0.00451 ( 26) link_BETA1-4 : angle 1.59350 ( 78) link_NAG-ASN : bond 0.00379 ( 40) link_NAG-ASN : angle 2.16054 ( 120) link_NAG-SER : bond 0.00069 ( 1) link_NAG-SER : angle 0.92597 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 186 PHE cc_start: 0.5312 (m-10) cc_final: 0.5069 (m-80) REVERT: A 455 LEU cc_start: 0.7071 (mm) cc_final: 0.6780 (mp) REVERT: A 465 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: A 1010 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: B 423 TYR cc_start: 0.4749 (t80) cc_final: 0.4425 (t80) REVERT: B 725 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 1017 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 190 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6254 (mmm160) REVERT: C 303 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8256 (tp) REVERT: C 370 ASN cc_start: 0.7101 (t0) cc_final: 0.6322 (p0) REVERT: C 773 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8178 (mt-10) REVERT: D 69 TRP cc_start: 0.1687 (t-100) cc_final: 0.0049 (t60) REVERT: D 249 MET cc_start: 0.2821 (mtt) cc_final: 0.2498 (mmt) REVERT: D 557 MET cc_start: 0.4292 (tmm) cc_final: 0.3048 (tpt) REVERT: F 270 MET cc_start: 0.5147 (mpp) cc_final: 0.4629 (mpp) REVERT: F 464 PHE cc_start: 0.3240 (OUTLIER) cc_final: 0.2889 (t80) REVERT: F 473 TRP cc_start: 0.3293 (m-90) cc_final: 0.2686 (m-90) outliers start: 50 outliers final: 37 residues processed: 187 average time/residue: 0.1920 time to fit residues: 63.9924 Evaluate side-chains 176 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 42 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 0.0770 chunk 117 optimal weight: 6.9990 chunk 442 optimal weight: 0.0670 overall best weight: 3.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.117906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083220 restraints weight = 171804.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.084320 restraints weight = 84729.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084886 restraints weight = 53844.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.085059 restraints weight = 44315.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085080 restraints weight = 42374.750| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 37728 Z= 0.197 Angle : 0.651 12.594 51428 Z= 0.324 Chirality : 0.045 0.395 5877 Planarity : 0.004 0.071 6494 Dihedral : 6.029 55.044 6508 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.33 % Favored : 92.56 % Rotamer: Outliers : 1.42 % Allowed : 17.88 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.97 (0.12), residues: 4450 helix: 0.86 (0.14), residues: 1447 sheet: 0.12 (0.22), residues: 606 loop : -1.89 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 634 TYR 0.021 0.001 TYR D 385 PHE 0.032 0.001 PHE D 369 TRP 0.045 0.001 TRP D 203 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00453 (37610) covalent geometry : angle 0.63435 (51138) SS BOND : bond 0.00330 ( 45) SS BOND : angle 1.50930 ( 90) hydrogen bonds : bond 0.04581 ( 1480) hydrogen bonds : angle 5.12227 ( 4153) Misc. bond : bond 0.00037 ( 6) link_BETA1-4 : bond 0.00517 ( 26) link_BETA1-4 : angle 1.66367 ( 78) link_NAG-ASN : bond 0.00528 ( 40) link_NAG-ASN : angle 2.52542 ( 120) link_NAG-SER : bond 0.00224 ( 1) link_NAG-SER : angle 1.79333 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8218.43 seconds wall clock time: 141 minutes 59.59 seconds (8519.59 seconds total)