Starting phenix.real_space_refine on Sun Jul 5 03:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.cif" model { file = "/net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb0_31048/07_2026/7eb0_31048.cif" } resolution = 3.6 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= 0.042 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 105 5.16 5 C 15855 2.51 5 N 4038 2.21 5 O 4948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24946 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7901 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 50, 'TRANS': 962} Chain breaks: 7 Chain: "B" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7918 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 50, 'TRANS': 964} Chain breaks: 7 Chain: "C" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 51, 'TRANS': 975} Chain breaks: 6 Chain: "D" 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 chiralities: 3 Chain: "E" 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 chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "X" 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 chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.20, per 1000 atoms: 0.21 Number of scatterers: 24946 At special positions: 0 Unit cell: (139.7, 140.8, 200.2, 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 105 16.00 O 4948 8.00 N 4038 7.00 C 15855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 234 " " NAG B2005 " - " ASN B 331 " " NAG B2006 " - " ASN B 603 " " NAG B2007 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 331 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 709 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5720 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.842A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.669A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.517A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.670A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.812A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 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 909 removed outlier: 3.613A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.615A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.554A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.231A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.722A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.569A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.590A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.706A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.531A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 909 removed outlier: 4.077A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.547A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.887A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.710A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.654A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.712A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.870A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.417A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.275A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 631 through 638 removed outlier: 4.260A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.008A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 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: 3.895A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 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 909 removed outlier: 3.779A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.552A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.579A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.276A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.657A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.833A 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: 3.989A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.859A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.690A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.229A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.718A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 541 removed outlier: 5.662A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.440A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.792A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.672A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.701A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.715A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.766A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.594A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.536A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.632A pdb=" N PHE B 192 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 170 through 172 removed outlier: 3.683A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.671A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.038A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.460A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.802A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 4.198A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.049A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.643A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.279A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.807A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.630A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.707A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 323 through 328 removed outlier: 6.330A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.822A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.617A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.735A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 6.929A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.768A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2385 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: 5.67 Time building geometry restraints manager: 3.19 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: 7857 1.34 - 1.47: 6529 1.47 - 1.59: 10973 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25488 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.58e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 ... (remaining 25483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 33443 1.58 - 3.17: 1065 3.17 - 4.75: 135 4.75 - 6.34: 39 6.34 - 7.92: 9 Bond angle restraints: 34691 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 111.12 117.40 -6.28 1.89e+00 2.80e-01 1.10e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 121.95 -7.55 2.30e+00 1.89e-01 1.08e+01 angle pdb=" N GLN C1002 " pdb=" CA GLN C1002 " pdb=" CB GLN C1002 " ideal model delta sigma weight residual 110.12 114.70 -4.58 1.47e+00 4.63e-01 9.71e+00 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 112.29 109.60 2.69 9.40e-01 1.13e+00 8.20e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.14 -3.44 1.22e+00 6.72e-01 7.96e+00 ... (remaining 34686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13111 17.78 - 35.57: 1146 35.57 - 53.35: 188 53.35 - 71.14: 42 71.14 - 88.92: 26 Dihedral angle restraints: 14513 sinusoidal: 5626 harmonic: 8887 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 1.62 -87.62 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 -179.58 -87.42 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -172.79 86.79 1 1.00e+01 1.00e-02 9.06e+01 ... (remaining 14510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4157 0.140 - 0.281: 22 0.281 - 0.421: 4 0.421 - 0.562: 2 0.562 - 0.702: 1 Chirality restraints: 4186 Sorted by residual: chirality pdb=" C1 NAG B2002 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B2002 " pdb=" O5 NAG B2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.88e+00 ... (remaining 4183 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 82 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 621 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 987 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.026 5.00e-02 4.00e+02 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1565 2.73 - 3.27: 24489 3.27 - 3.82: 38240 3.82 - 4.36: 42204 4.36 - 4.90: 75648 Nonbonded interactions: 182146 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.188 3.040 nonbonded pdb=" OE2 GLU C 725 " pdb=" NE2 HIS C1064 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.209 3.040 nonbonded pdb=" O3 NAG B2002 " pdb=" O7 NAG B2002 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.247 3.040 ... (remaining 182141 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 27 through 827 or resid 855 through 2005)) selection = (chain 'C' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 2005)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 23.100 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 0.055 25602 Z= 0.205 Angle : 0.727 21.426 34998 Z= 0.342 Chirality : 0.051 0.702 4186 Planarity : 0.004 0.049 4381 Dihedral : 13.880 88.920 8688 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3009 helix: 1.47 (0.21), residues: 662 sheet: -0.48 (0.20), residues: 656 loop : -1.87 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.018 0.001 TYR C 160 PHE 0.023 0.001 PHE A 906 TRP 0.008 0.001 TRP A 64 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (25488) covalent geometry : angle 0.65534 / 0.33 (34691) SS BOND : bond 0.00483 / 0.28 ( 35) SS BOND : angle 1.52524 / 0.98 ( 70) hydrogen bonds : bond 0.14003 / 9.29 ( 886) hydrogen bonds : angle 6.04625 / 4.11 ( 2385) link_BETA1-4 : bond 0.00725 / 0.47 ( 32) link_BETA1-4 : angle 3.56855 / 2.84 ( 96) link_NAG-ASN : bond 0.00690 / 0.47 ( 47) link_NAG-ASN : angle 3.97481 / 2.45 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 731 MET cc_start: 0.9076 (ptm) cc_final: 0.8845 (ptt) REVERT: B 869 MET cc_start: 0.8255 (mtt) cc_final: 0.8036 (mtt) REVERT: B 1002 GLN cc_start: 0.7673 (tm130) cc_final: 0.7346 (tm-30) REVERT: C 869 MET cc_start: 0.8758 (mmm) cc_final: 0.8481 (mmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1391 time to fit residues: 28.4022 Evaluate side-chains 89 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067188 restraints weight = 64175.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070131 restraints weight = 35880.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072050 restraints weight = 25694.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073305 restraints weight = 20944.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074102 restraints weight = 18372.818| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25602 Z= 0.162 Angle : 0.666 20.839 34998 Z= 0.319 Chirality : 0.047 0.640 4186 Planarity : 0.004 0.048 4381 Dihedral : 4.268 25.641 3264 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 0.34 % Allowed : 6.33 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 3009 helix: 1.52 (0.21), residues: 666 sheet: -0.45 (0.20), residues: 636 loop : -1.88 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.014 0.001 TYR A 91 PHE 0.028 0.001 PHE C 456 TRP 0.011 0.001 TRP A 353 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (25488) covalent geometry : angle 0.60682 / 0.31 (34691) SS BOND : bond 0.00433 / 0.29 ( 35) SS BOND : angle 1.43888 / 0.98 ( 70) hydrogen bonds : bond 0.05615 / 3.66 ( 886) hydrogen bonds : angle 5.17054 / 3.54 ( 2385) link_BETA1-4 : bond 0.00686 / 0.43 ( 32) link_BETA1-4 : angle 2.60306 / 2.03 ( 96) link_NAG-ASN : bond 0.00597 / 0.41 ( 47) link_NAG-ASN : angle 3.71868 / 2.27 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9076 (tmm) cc_final: 0.8084 (tmm) REVERT: B 1002 GLN cc_start: 0.7704 (tm130) cc_final: 0.7412 (tm-30) REVERT: B 1029 MET cc_start: 0.9004 (tmm) cc_final: 0.8219 (tmm) REVERT: C 869 MET cc_start: 0.8755 (mmm) cc_final: 0.8446 (mmm) REVERT: C 895 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: C 918 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7207 (mt-10) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.1367 time to fit residues: 23.7430 Evaluate side-chains 89 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 171 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 291 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C1005 GLN ** C1106 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 = 0.3855 r_free = 0.3855 target = 0.107631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067832 restraints weight = 64084.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070785 restraints weight = 35544.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072739 restraints weight = 25443.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074018 restraints weight = 20679.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074839 restraints weight = 18092.433| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25602 Z= 0.127 Angle : 0.623 20.758 34998 Z= 0.295 Chirality : 0.046 0.572 4186 Planarity : 0.004 0.050 4381 Dihedral : 4.098 22.649 3264 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 0.67 % Allowed : 9.18 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3009 helix: 1.56 (0.21), residues: 673 sheet: -0.29 (0.21), residues: 614 loop : -1.81 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.012 0.001 TYR B 91 PHE 0.017 0.001 PHE C 456 TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25488) covalent geometry : angle 0.56459 / 0.28 (34691) SS BOND : bond 0.00398 / 0.26 ( 35) SS BOND : angle 1.31088 / 0.85 ( 70) hydrogen bonds : bond 0.05135 / 3.33 ( 886) hydrogen bonds : angle 4.89810 / 3.36 ( 2385) link_BETA1-4 : bond 0.00706 / 0.44 ( 32) link_BETA1-4 : angle 2.54743 / 1.98 ( 96) link_NAG-ASN : bond 0.00611 / 0.42 ( 47) link_NAG-ASN : angle 3.55935 / 2.18 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9091 (tmm) cc_final: 0.8093 (tmm) REVERT: B 1002 GLN cc_start: 0.7692 (tm130) cc_final: 0.7395 (tm-30) REVERT: B 1029 MET cc_start: 0.9015 (tmm) cc_final: 0.8242 (tmm) REVERT: C 869 MET cc_start: 0.8759 (mmm) cc_final: 0.8376 (mmm) REVERT: C 895 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: C 918 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7259 (mt-10) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 0.1441 time to fit residues: 27.8660 Evaluate side-chains 95 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 152 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.106223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066275 restraints weight = 64047.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069171 restraints weight = 35829.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071016 restraints weight = 25699.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072275 restraints weight = 21069.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073068 restraints weight = 18518.827| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25602 Z= 0.174 Angle : 0.653 20.500 34998 Z= 0.312 Chirality : 0.047 0.583 4186 Planarity : 0.004 0.050 4381 Dihedral : 4.219 21.756 3264 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 0.94 % Allowed : 12.03 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 3009 helix: 1.44 (0.21), residues: 681 sheet: -0.47 (0.20), residues: 641 loop : -1.87 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 995 TYR 0.014 0.001 TYR B 91 PHE 0.021 0.001 PHE B 377 TRP 0.010 0.001 TRP A 353 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (25488) covalent geometry : angle 0.59885 / 0.30 (34691) SS BOND : bond 0.00368 / 0.25 ( 35) SS BOND : angle 1.43157 / 0.99 ( 70) hydrogen bonds : bond 0.05559 / 3.61 ( 886) hydrogen bonds : angle 4.95294 / 3.40 ( 2385) link_BETA1-4 : bond 0.00649 / 0.40 ( 32) link_BETA1-4 : angle 2.49373 / 1.94 ( 96) link_NAG-ASN : bond 0.00566 / 0.40 ( 47) link_NAG-ASN : angle 3.51838 / 2.17 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9118 (tmm) cc_final: 0.8160 (tmm) REVERT: B 518 LEU cc_start: 0.8174 (mt) cc_final: 0.7958 (mp) REVERT: B 1002 GLN cc_start: 0.7771 (tm130) cc_final: 0.7429 (tm-30) REVERT: B 1029 MET cc_start: 0.9057 (tmm) cc_final: 0.8221 (tmm) REVERT: C 869 MET cc_start: 0.8810 (mmm) cc_final: 0.8385 (mmm) REVERT: C 918 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7246 (mp0) outliers start: 25 outliers final: 17 residues processed: 108 average time/residue: 0.1349 time to fit residues: 25.6659 Evaluate side-chains 98 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 89 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 222 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 189 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 919 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 919 ASN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.111311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070813 restraints weight = 62449.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073832 restraints weight = 34910.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075794 restraints weight = 25089.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077072 restraints weight = 20514.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077915 restraints weight = 18053.505| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25602 Z= 0.108 Angle : 0.613 20.674 34998 Z= 0.287 Chirality : 0.046 0.565 4186 Planarity : 0.004 0.051 4381 Dihedral : 3.988 21.581 3264 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 1.24 % Allowed : 13.15 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3009 helix: 1.67 (0.21), residues: 675 sheet: -0.28 (0.21), residues: 618 loop : -1.77 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.014 0.001 TYR B1067 PHE 0.012 0.001 PHE A 238 TRP 0.013 0.001 TRP B 104 HIS 0.007 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (25488) covalent geometry : angle 0.55868 / 0.27 (34691) SS BOND : bond 0.00349 / 0.22 ( 35) SS BOND : angle 1.20745 / 0.76 ( 70) hydrogen bonds : bond 0.04806 / 3.11 ( 886) hydrogen bonds : angle 4.71870 / 3.25 ( 2385) link_BETA1-4 : bond 0.00746 / 0.47 ( 32) link_BETA1-4 : angle 2.44917 / 1.90 ( 96) link_NAG-ASN : bond 0.00610 / 0.42 ( 47) link_NAG-ASN : angle 3.41934 / 2.10 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.7638 (tm130) cc_final: 0.7300 (tm-30) REVERT: B 1029 MET cc_start: 0.9111 (tmm) cc_final: 0.8286 (tmm) REVERT: C 418 ILE cc_start: 0.8371 (mp) cc_final: 0.8131 (tp) REVERT: C 869 MET cc_start: 0.8704 (mmm) cc_final: 0.8275 (mmm) REVERT: C 918 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7070 (mp0) outliers start: 33 outliers final: 18 residues processed: 125 average time/residue: 0.1410 time to fit residues: 31.1905 Evaluate side-chains 101 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 300 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 191 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN A 872 GLN B 481 ASN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.107922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068101 restraints weight = 63752.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071072 restraints weight = 35019.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073080 restraints weight = 24936.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074384 restraints weight = 20163.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075224 restraints weight = 17637.355| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25602 Z= 0.111 Angle : 0.613 20.592 34998 Z= 0.287 Chirality : 0.045 0.556 4186 Planarity : 0.004 0.050 4381 Dihedral : 3.910 20.919 3264 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 1.20 % Allowed : 14.05 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3009 helix: 1.68 (0.21), residues: 671 sheet: -0.27 (0.21), residues: 625 loop : -1.70 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.015 0.001 TYR A 200 PHE 0.014 0.001 PHE B 456 TRP 0.014 0.001 TRP B 64 HIS 0.006 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (25488) covalent geometry : angle 0.56028 / 0.27 (34691) SS BOND : bond 0.00325 / 0.20 ( 35) SS BOND : angle 1.16808 / 0.76 ( 70) hydrogen bonds : bond 0.04667 / 3.02 ( 886) hydrogen bonds : angle 4.62961 / 3.19 ( 2385) link_BETA1-4 : bond 0.00703 / 0.44 ( 32) link_BETA1-4 : angle 2.39944 / 1.87 ( 96) link_NAG-ASN : bond 0.00585 / 0.41 ( 47) link_NAG-ASN : angle 3.38262 / 2.08 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9036 (tmm) cc_final: 0.8085 (tmm) REVERT: B 518 LEU cc_start: 0.8137 (mt) cc_final: 0.7921 (mp) REVERT: B 1002 GLN cc_start: 0.7611 (tm130) cc_final: 0.7260 (tm-30) REVERT: B 1029 MET cc_start: 0.9144 (tmm) cc_final: 0.8340 (tmm) REVERT: C 418 ILE cc_start: 0.8478 (mp) cc_final: 0.8269 (tp) REVERT: C 869 MET cc_start: 0.8723 (mmm) cc_final: 0.8435 (mmm) REVERT: C 918 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7217 (mp0) outliers start: 32 outliers final: 24 residues processed: 115 average time/residue: 0.1378 time to fit residues: 28.0637 Evaluate side-chains 112 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 1 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 135 optimal weight: 0.6980 chunk 12 optimal weight: 0.0010 chunk 55 optimal weight: 8.9990 chunk 220 optimal weight: 0.3980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.112583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072085 restraints weight = 62186.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075129 restraints weight = 34700.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077143 restraints weight = 24941.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078451 restraints weight = 20332.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079262 restraints weight = 17892.363| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25602 Z= 0.102 Angle : 0.604 20.637 34998 Z= 0.282 Chirality : 0.045 0.549 4186 Planarity : 0.004 0.050 4381 Dihedral : 3.812 20.677 3264 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 1.12 % Allowed : 14.54 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3009 helix: 1.75 (0.21), residues: 663 sheet: -0.19 (0.21), residues: 625 loop : -1.65 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.014 0.001 TYR B1067 PHE 0.022 0.001 PHE B 377 TRP 0.011 0.001 TRP B 104 HIS 0.006 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (25488) covalent geometry : angle 0.55262 / 0.27 (34691) SS BOND : bond 0.00310 / 0.19 ( 35) SS BOND : angle 1.09276 / 0.73 ( 70) hydrogen bonds : bond 0.04371 / 2.83 ( 886) hydrogen bonds : angle 4.53892 / 3.12 ( 2385) link_BETA1-4 : bond 0.00711 / 0.45 ( 32) link_BETA1-4 : angle 2.35220 / 1.83 ( 96) link_NAG-ASN : bond 0.00602 / 0.42 ( 47) link_NAG-ASN : angle 3.34171 / 2.05 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9074 (tmm) cc_final: 0.8166 (tmm) REVERT: B 1002 GLN cc_start: 0.7541 (tm130) cc_final: 0.7215 (tm-30) REVERT: B 1029 MET cc_start: 0.9155 (tmm) cc_final: 0.8346 (tmm) REVERT: C 869 MET cc_start: 0.8687 (mmm) cc_final: 0.8411 (mmm) REVERT: C 918 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: C 960 ASN cc_start: 0.9168 (t0) cc_final: 0.8823 (t0) outliers start: 30 outliers final: 24 residues processed: 120 average time/residue: 0.1407 time to fit residues: 30.0541 Evaluate side-chains 114 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 14 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 278 optimal weight: 0.8980 chunk 271 optimal weight: 0.0370 chunk 137 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN C1005 GLN ** C1106 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 = 0.3884 r_free = 0.3884 target = 0.112534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071958 restraints weight = 61838.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074943 restraints weight = 34835.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076915 restraints weight = 25172.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.078206 restraints weight = 20629.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078973 restraints weight = 18142.983| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25602 Z= 0.110 Angle : 0.605 20.550 34998 Z= 0.283 Chirality : 0.045 0.542 4186 Planarity : 0.003 0.049 4381 Dihedral : 3.803 20.227 3264 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 1.46 % Allowed : 14.65 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3009 helix: 1.74 (0.21), residues: 668 sheet: -0.20 (0.21), residues: 630 loop : -1.63 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.015 0.001 TYR B1067 PHE 0.021 0.001 PHE B 377 TRP 0.009 0.001 TRP B 104 HIS 0.005 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (25488) covalent geometry : angle 0.55423 / 0.27 (34691) SS BOND : bond 0.00472 / 0.27 ( 35) SS BOND : angle 1.28237 / 0.85 ( 70) hydrogen bonds : bond 0.04400 / 2.85 ( 886) hydrogen bonds : angle 4.52984 / 3.11 ( 2385) link_BETA1-4 : bond 0.00690 / 0.43 ( 32) link_BETA1-4 : angle 2.29948 / 1.80 ( 96) link_NAG-ASN : bond 0.00576 / 0.41 ( 47) link_NAG-ASN : angle 3.31191 / 2.04 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9102 (tmm) cc_final: 0.8171 (tmm) REVERT: B 518 LEU cc_start: 0.8129 (mt) cc_final: 0.7910 (mp) REVERT: B 1002 GLN cc_start: 0.7557 (tm130) cc_final: 0.7232 (tm-30) REVERT: B 1029 MET cc_start: 0.9181 (tmm) cc_final: 0.8393 (tmm) REVERT: C 869 MET cc_start: 0.8711 (mmm) cc_final: 0.8427 (mmm) REVERT: C 918 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: C 960 ASN cc_start: 0.9167 (t0) cc_final: 0.8821 (t0) REVERT: C 1027 THR cc_start: 0.8768 (m) cc_final: 0.8244 (p) outliers start: 39 outliers final: 26 residues processed: 125 average time/residue: 0.1466 time to fit residues: 31.9764 Evaluate side-chains 116 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 100 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 137 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 218 optimal weight: 3.9990 chunk 246 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072106 restraints weight = 61871.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075088 restraints weight = 34899.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.077088 restraints weight = 25203.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078328 restraints weight = 20633.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079181 restraints weight = 18204.739| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25602 Z= 0.109 Angle : 0.607 20.538 34998 Z= 0.284 Chirality : 0.045 0.538 4186 Planarity : 0.004 0.049 4381 Dihedral : 3.786 19.827 3264 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.27 % Allowed : 15.02 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3009 helix: 1.73 (0.21), residues: 671 sheet: -0.19 (0.21), residues: 632 loop : -1.61 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.016 0.001 TYR A 200 PHE 0.011 0.001 PHE C 392 TRP 0.011 0.001 TRP B 353 HIS 0.005 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (25488) covalent geometry : angle 0.55664 / 0.27 (34691) SS BOND : bond 0.00378 / 0.22 ( 35) SS BOND : angle 1.38865 / 0.86 ( 70) hydrogen bonds : bond 0.04340 / 2.82 ( 886) hydrogen bonds : angle 4.51813 / 3.10 ( 2385) link_BETA1-4 : bond 0.00695 / 0.43 ( 32) link_BETA1-4 : angle 2.23878 / 1.76 ( 96) link_NAG-ASN : bond 0.00581 / 0.41 ( 47) link_NAG-ASN : angle 3.29123 / 2.03 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9119 (tmm) cc_final: 0.8254 (tmm) REVERT: B 518 LEU cc_start: 0.8038 (mt) cc_final: 0.7807 (mp) REVERT: B 1002 GLN cc_start: 0.7539 (tm130) cc_final: 0.7215 (tm-30) REVERT: B 1029 MET cc_start: 0.9187 (tmm) cc_final: 0.8364 (tmm) REVERT: C 773 GLU cc_start: 0.8256 (tp30) cc_final: 0.8036 (tp30) REVERT: C 869 MET cc_start: 0.8687 (mmm) cc_final: 0.8431 (mmm) REVERT: C 872 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8222 (tp40) REVERT: C 918 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: C 960 ASN cc_start: 0.9207 (t0) cc_final: 0.8858 (t0) REVERT: C 1027 THR cc_start: 0.8751 (m) cc_final: 0.8230 (p) outliers start: 34 outliers final: 27 residues processed: 122 average time/residue: 0.1348 time to fit residues: 29.0242 Evaluate side-chains 117 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 102 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.110201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069204 restraints weight = 62545.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071989 restraints weight = 36091.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073849 restraints weight = 26485.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075052 restraints weight = 21856.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075765 restraints weight = 19390.563| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25602 Z= 0.207 Angle : 0.676 20.120 34998 Z= 0.325 Chirality : 0.047 0.536 4186 Planarity : 0.004 0.047 4381 Dihedral : 4.137 19.701 3264 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 1.16 % Allowed : 15.51 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3009 helix: 1.42 (0.21), residues: 684 sheet: -0.44 (0.20), residues: 659 loop : -1.73 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.017 0.001 TYR A 200 PHE 0.022 0.002 PHE B1121 TRP 0.009 0.002 TRP A 64 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (25488) covalent geometry : angle 0.63003 / 0.31 (34691) SS BOND : bond 0.00436 / 0.27 ( 35) SS BOND : angle 1.62021 / 1.05 ( 70) hydrogen bonds : bond 0.05476 / 3.57 ( 886) hydrogen bonds : angle 4.82944 / 3.32 ( 2385) link_BETA1-4 : bond 0.00644 / 0.40 ( 32) link_BETA1-4 : angle 2.19340 / 1.74 ( 96) link_NAG-ASN : bond 0.00554 / 0.40 ( 47) link_NAG-ASN : angle 3.33702 / 2.07 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9116 (tmm) cc_final: 0.8079 (tmm) REVERT: B 518 LEU cc_start: 0.8175 (mt) cc_final: 0.7944 (mp) REVERT: B 1002 GLN cc_start: 0.7832 (tm130) cc_final: 0.7480 (tm-30) REVERT: B 1029 MET cc_start: 0.9153 (tmm) cc_final: 0.8253 (tmm) REVERT: C 869 MET cc_start: 0.8785 (mmm) cc_final: 0.8510 (mmm) REVERT: C 918 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7496 (mt-10) outliers start: 31 outliers final: 25 residues processed: 110 average time/residue: 0.1323 time to fit residues: 26.0553 Evaluate side-chains 106 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 232 optimal weight: 0.0170 chunk 281 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.111226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070532 restraints weight = 61936.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073431 restraints weight = 35296.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075292 restraints weight = 25664.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076551 restraints weight = 21155.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077337 restraints weight = 18695.730| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25602 Z= 0.130 Angle : 0.631 20.397 34998 Z= 0.299 Chirality : 0.046 0.535 4186 Planarity : 0.004 0.049 4381 Dihedral : 3.996 20.536 3264 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 1.16 % Allowed : 15.66 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 3009 helix: 1.52 (0.21), residues: 678 sheet: -0.41 (0.21), residues: 639 loop : -1.69 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.015 0.001 TYR A 200 PHE 0.013 0.001 PHE A1121 TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (25488) covalent geometry : angle 0.58367 / 0.29 (34691) SS BOND : bond 0.00373 / 0.23 ( 35) SS BOND : angle 1.44326 / 0.92 ( 70) hydrogen bonds : bond 0.04907 / 3.19 ( 886) hydrogen bonds : angle 4.69039 / 3.23 ( 2385) link_BETA1-4 : bond 0.00697 / 0.44 ( 32) link_BETA1-4 : angle 2.14053 / 1.70 ( 96) link_NAG-ASN : bond 0.00580 / 0.41 ( 47) link_NAG-ASN : angle 3.28859 / 2.03 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4774.84 seconds wall clock time: 83 minutes 10.47 seconds (4990.47 seconds total)