Starting phenix.real_space_refine on Thu Mar 5 20:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eb0_31048/03_2026/7eb0_31048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb0_31048/03_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_31048/03_2026/7eb0_31048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb0_31048/03_2026/7eb0_31048.map" model { file = "/net/cci-nas-00/data/ceres_data/7eb0_31048/03_2026/7eb0_31048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb0_31048/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 15 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.73, per 1000 atoms: 0.23 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: 1.98 Conformation dependent library (CDL) restraints added in 974.2 milliseconds 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: 0.73 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: 5.27 Time building geometry restraints manager: 2.64 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 - 23.27: 15101 23.27 - 46.54: 858 46.54 - 69.81: 135 69.81 - 93.08: 48 93.08 - 116.35: 45 Dihedral angle restraints: 16187 sinusoidal: 7300 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 16184 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.650 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 15.820 116.346 10362 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 covalent geometry : bond 0.00433 (25488) covalent geometry : angle 0.65534 (34691) SS BOND : bond 0.00483 ( 35) SS BOND : angle 1.52524 ( 70) hydrogen bonds : bond 0.14003 ( 886) hydrogen bonds : angle 6.04625 ( 2385) link_BETA1-4 : bond 0.00725 ( 32) link_BETA1-4 : angle 3.56855 ( 96) link_NAG-ASN : bond 0.00690 ( 47) link_NAG-ASN : angle 3.97481 ( 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 : 0.891 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: 0.1374 time to fit residues: 28.1901 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 : 0.799 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.107005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067229 restraints weight = 64165.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070165 restraints weight = 35809.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072030 restraints weight = 25634.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073312 restraints weight = 20969.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074137 restraints weight = 18386.261| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.0638 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 : 0.678 21.020 34998 Z= 0.321 Chirality : 0.048 0.656 4186 Planarity : 0.004 0.048 4381 Dihedral : 11.671 109.899 4938 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 0.30 % Allowed : 5.92 % Favored : 93.78 % 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: -1.11 (0.15), residues: 3009 helix: 1.52 (0.21), residues: 666 sheet: -0.45 (0.20), residues: 636 loop : -1.87 (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 0.027 0.001 PHE C 456 TRP 0.012 0.001 TRP A 353 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00377 (25488) covalent geometry : angle 0.61576 (34691) SS BOND : bond 0.00403 ( 35) SS BOND : angle 1.44371 ( 70) hydrogen bonds : bond 0.05715 ( 886) hydrogen bonds : angle 5.19215 ( 2385) link_BETA1-4 : bond 0.00736 ( 32) link_BETA1-4 : angle 2.87218 ( 96) link_NAG-ASN : bond 0.00613 ( 47) link_NAG-ASN : angle 3.76051 ( 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 101 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9033 (ptm) cc_final: 0.8771 (ptt) REVERT: A 1029 MET cc_start: 0.9090 (tmm) cc_final: 0.8081 (tmm) REVERT: B 1002 GLN cc_start: 0.7704 (tm130) cc_final: 0.7413 (tm-30) REVERT: B 1029 MET cc_start: 0.8999 (tmm) cc_final: 0.8222 (tmm) REVERT: C 869 MET cc_start: 0.8752 (mmm) cc_final: 0.8440 (mmm) REVERT: C 895 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: C 918 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7226 (mt-10) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.1375 time to fit residues: 23.9476 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 : 0.899 ------------------------------------------------------------------------------- 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: 0.0470 chunk 292 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 544 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.107829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068008 restraints weight = 64095.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.070994 restraints weight = 35509.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072950 restraints weight = 25338.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074240 restraints weight = 20597.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.075060 restraints weight = 18030.696| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25602 Z= 0.123 Angle : 0.641 20.919 34998 Z= 0.299 Chirality : 0.047 0.615 4186 Planarity : 0.004 0.050 4381 Dihedral : 10.070 109.168 4938 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 0.60 % Allowed : 9.14 % Favored : 90.26 % 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: -0.99 (0.15), residues: 3009 helix: 1.63 (0.21), residues: 667 sheet: -0.30 (0.21), residues: 616 loop : -1.81 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.012 0.001 TYR C 369 PHE 0.016 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 covalent geometry : bond 0.00277 (25488) covalent geometry : angle 0.57852 (34691) SS BOND : bond 0.00406 ( 35) SS BOND : angle 1.33929 ( 70) hydrogen bonds : bond 0.05053 ( 886) hydrogen bonds : angle 4.87876 ( 2385) link_BETA1-4 : bond 0.00731 ( 32) link_BETA1-4 : angle 2.91519 ( 96) link_NAG-ASN : bond 0.00621 ( 47) link_NAG-ASN : angle 3.62085 ( 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 118 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9088 (tmm) cc_final: 0.8082 (tmm) REVERT: B 819 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8279 (mm-30) REVERT: B 1002 GLN cc_start: 0.7690 (tm130) cc_final: 0.7383 (tm-30) REVERT: B 1029 MET cc_start: 0.9002 (tmm) cc_final: 0.8222 (tmm) REVERT: C 869 MET cc_start: 0.8795 (mmm) cc_final: 0.8395 (mmm) REVERT: C 895 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: C 918 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7231 (mt-10) outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 0.1314 time to fit residues: 26.0091 Evaluate side-chains 97 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 7.9990 chunk 169 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 126 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3854 r_free = 0.3854 target = 0.107591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067771 restraints weight = 63735.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070719 restraints weight = 35517.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072671 restraints weight = 25460.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073894 restraints weight = 20724.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074760 restraints weight = 18212.829| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25602 Z= 0.127 Angle : 0.641 20.897 34998 Z= 0.297 Chirality : 0.047 0.617 4186 Planarity : 0.004 0.049 4381 Dihedral : 9.292 105.528 4938 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 0.90 % Allowed : 11.28 % Favored : 87.82 % 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: -0.97 (0.15), residues: 3009 helix: 1.64 (0.21), residues: 671 sheet: -0.33 (0.21), residues: 631 loop : -1.80 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.013 0.001 TYR C 369 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 covalent geometry : bond 0.00289 (25488) covalent geometry : angle 0.57861 (34691) SS BOND : bond 0.00387 ( 35) SS BOND : angle 1.30476 ( 70) hydrogen bonds : bond 0.04970 ( 886) hydrogen bonds : angle 4.78901 ( 2385) link_BETA1-4 : bond 0.00710 ( 32) link_BETA1-4 : angle 2.94826 ( 96) link_NAG-ASN : bond 0.00595 ( 47) link_NAG-ASN : angle 3.57113 ( 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 118 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9102 (tmm) cc_final: 0.8170 (tmm) REVERT: B 1002 GLN cc_start: 0.7633 (tm130) cc_final: 0.7324 (tm-30) REVERT: B 1029 MET cc_start: 0.9067 (tmm) cc_final: 0.8261 (tmm) REVERT: C 869 MET cc_start: 0.8748 (mmm) cc_final: 0.8347 (mmm) REVERT: C 895 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: C 918 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7328 (mt-10) outliers start: 24 outliers final: 16 residues processed: 112 average time/residue: 0.1246 time to fit residues: 24.8657 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 : 0.794 ------------------------------------------------------------------------------- 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: 0.9980 chunk 247 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 222 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 7.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3869 r_free = 0.3869 target = 0.108533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068728 restraints weight = 63646.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071781 restraints weight = 34732.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073802 restraints weight = 24637.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075070 restraints weight = 19918.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075960 restraints weight = 17420.105| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1227 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= 0.106 Angle : 0.629 20.913 34998 Z= 0.289 Chirality : 0.046 0.610 4186 Planarity : 0.004 0.049 4381 Dihedral : 8.740 97.641 4938 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 1.09 % Allowed : 12.70 % Favored : 86.21 % 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: -0.85 (0.15), residues: 3009 helix: 1.70 (0.21), residues: 669 sheet: -0.24 (0.21), residues: 620 loop : -1.70 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.013 0.001 TYR B1067 PHE 0.012 0.001 PHE B 759 TRP 0.010 0.001 TRP B 104 HIS 0.007 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00230 (25488) covalent geometry : angle 0.56827 (34691) SS BOND : bond 0.00332 ( 35) SS BOND : angle 1.15974 ( 70) hydrogen bonds : bond 0.04577 ( 886) hydrogen bonds : angle 4.64071 ( 2385) link_BETA1-4 : bond 0.00739 ( 32) link_BETA1-4 : angle 2.95205 ( 96) link_NAG-ASN : bond 0.00610 ( 47) link_NAG-ASN : angle 3.50118 ( 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 124 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8527 (t60) cc_final: 0.7647 (t60) REVERT: B 1002 GLN cc_start: 0.7581 (tm130) cc_final: 0.7256 (tm-30) REVERT: B 1029 MET cc_start: 0.9136 (tmm) cc_final: 0.8359 (tmm) REVERT: C 869 MET cc_start: 0.8713 (mmm) cc_final: 0.8407 (mmm) REVERT: C 918 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7299 (mt-10) outliers start: 29 outliers final: 13 residues processed: 118 average time/residue: 0.1442 time to fit residues: 29.5844 Evaluate side-chains 99 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 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 620 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 300 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 154 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 872 GLN C1005 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.108169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068424 restraints weight = 63663.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071458 restraints weight = 34856.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073443 restraints weight = 24712.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074761 restraints weight = 19975.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075575 restraints weight = 17448.581| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25602 Z= 0.113 Angle : 0.634 20.784 34998 Z= 0.291 Chirality : 0.046 0.606 4186 Planarity : 0.003 0.049 4381 Dihedral : 8.372 95.721 4938 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 1.24 % Allowed : 13.41 % Favored : 85.35 % 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: -0.81 (0.15), residues: 3009 helix: 1.67 (0.21), residues: 672 sheet: -0.22 (0.21), residues: 629 loop : -1.66 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.014 0.001 TYR A 200 PHE 0.012 0.001 PHE A1121 TRP 0.009 0.001 TRP A 353 HIS 0.006 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00253 (25488) covalent geometry : angle 0.57406 (34691) SS BOND : bond 0.00313 ( 35) SS BOND : angle 1.16178 ( 70) hydrogen bonds : bond 0.04562 ( 886) hydrogen bonds : angle 4.59295 ( 2385) link_BETA1-4 : bond 0.00725 ( 32) link_BETA1-4 : angle 2.96777 ( 96) link_NAG-ASN : bond 0.00581 ( 47) link_NAG-ASN : angle 3.47840 ( 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 122 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9032 (tmm) cc_final: 0.8022 (tmm) REVERT: B 64 TRP cc_start: 0.8535 (t60) cc_final: 0.7684 (t60) REVERT: B 518 LEU cc_start: 0.7981 (mt) cc_final: 0.7774 (mp) REVERT: B 1002 GLN cc_start: 0.7571 (tm130) cc_final: 0.7262 (tm-30) REVERT: B 1029 MET cc_start: 0.9113 (tmm) cc_final: 0.8319 (tmm) REVERT: C 869 MET cc_start: 0.8726 (mmm) cc_final: 0.8432 (mmm) REVERT: C 918 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7413 (mt-10) outliers start: 33 outliers final: 20 residues processed: 115 average time/residue: 0.1375 time to fit residues: 28.1468 Evaluate side-chains 106 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 950 ASP 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 902 MET Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 1 optimal weight: 0.9990 chunk 291 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 0.0060 chunk 135 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 220 optimal weight: 0.0170 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 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 = 0.3872 r_free = 0.3872 target = 0.108765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069095 restraints weight = 63465.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072157 restraints weight = 34657.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074074 restraints weight = 24548.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075454 restraints weight = 19918.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076343 restraints weight = 17379.722| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25602 Z= 0.104 Angle : 0.627 20.736 34998 Z= 0.287 Chirality : 0.046 0.600 4186 Planarity : 0.003 0.049 4381 Dihedral : 8.025 93.296 4938 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 1.05 % Allowed : 13.98 % Favored : 84.98 % 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: 1.76 (0.21), residues: 664 sheet: -0.16 (0.21), residues: 628 loop : -1.62 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.014 0.001 TYR B1067 PHE 0.017 0.001 PHE A 515 TRP 0.009 0.001 TRP B 104 HIS 0.006 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00226 (25488) covalent geometry : angle 0.56638 (34691) SS BOND : bond 0.00339 ( 35) SS BOND : angle 1.30052 ( 70) hydrogen bonds : bond 0.04342 ( 886) hydrogen bonds : angle 4.53083 ( 2385) link_BETA1-4 : bond 0.00727 ( 32) link_BETA1-4 : angle 2.94366 ( 96) link_NAG-ASN : bond 0.00587 ( 47) link_NAG-ASN : angle 3.44667 ( 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 123 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9059 (tmm) cc_final: 0.8114 (tmm) REVERT: B 64 TRP cc_start: 0.8539 (t60) cc_final: 0.7691 (t60) REVERT: B 1002 GLN cc_start: 0.7532 (tm130) cc_final: 0.7216 (tm-30) REVERT: B 1029 MET cc_start: 0.9170 (tmm) cc_final: 0.8365 (tmm) REVERT: C 869 MET cc_start: 0.8708 (mmm) cc_final: 0.8431 (mmm) REVERT: C 918 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: C 960 ASN cc_start: 0.9182 (t0) cc_final: 0.8833 (t0) REVERT: C 1027 THR cc_start: 0.8757 (m) cc_final: 0.8254 (p) outliers start: 28 outliers final: 20 residues processed: 116 average time/residue: 0.1319 time to fit residues: 27.1022 Evaluate side-chains 111 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 705 VAL 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 432 CYS 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 902 MET Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 14 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 278 optimal weight: 0.0980 chunk 271 optimal weight: 0.4980 chunk 137 optimal weight: 20.0000 chunk 63 optimal weight: 0.0170 chunk 287 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.109028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069459 restraints weight = 63300.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072565 restraints weight = 34609.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074593 restraints weight = 24424.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075934 restraints weight = 19656.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076813 restraints weight = 17138.958| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25602 Z= 0.104 Angle : 0.624 20.701 34998 Z= 0.286 Chirality : 0.046 0.588 4186 Planarity : 0.004 0.048 4381 Dihedral : 7.673 88.922 4938 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 1.09 % Allowed : 14.42 % Favored : 84.49 % 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: -0.69 (0.15), residues: 3009 helix: 1.77 (0.21), residues: 666 sheet: -0.10 (0.21), residues: 618 loop : -1.58 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.014 0.001 TYR B1067 PHE 0.022 0.001 PHE B 377 TRP 0.015 0.001 TRP B 353 HIS 0.005 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00226 (25488) covalent geometry : angle 0.56529 (34691) SS BOND : bond 0.00361 ( 35) SS BOND : angle 1.18529 ( 70) hydrogen bonds : bond 0.04224 ( 886) hydrogen bonds : angle 4.49280 ( 2385) link_BETA1-4 : bond 0.00706 ( 32) link_BETA1-4 : angle 2.89470 ( 96) link_NAG-ASN : bond 0.00583 ( 47) link_NAG-ASN : angle 3.41444 ( 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 129 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.8528 (t60) cc_final: 0.7687 (t60) REVERT: B 1002 GLN cc_start: 0.7495 (tm130) cc_final: 0.7139 (tm-30) REVERT: B 1029 MET cc_start: 0.9184 (tmm) cc_final: 0.8405 (tmm) REVERT: C 869 MET cc_start: 0.8687 (mmm) cc_final: 0.8447 (mmm) REVERT: C 872 GLN cc_start: 0.8423 (tp40) cc_final: 0.8203 (tp40) REVERT: C 918 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: C 960 ASN cc_start: 0.9211 (t0) cc_final: 0.8854 (t0) REVERT: C 1027 THR cc_start: 0.8751 (m) cc_final: 0.8278 (p) outliers start: 29 outliers final: 23 residues processed: 123 average time/residue: 0.1352 time to fit residues: 29.5148 Evaluate side-chains 116 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR 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 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 902 MET Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 100 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 272 optimal weight: 0.0970 chunk 181 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3821 r_free = 0.3821 target = 0.105373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065559 restraints weight = 64227.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068356 restraints weight = 36157.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.070137 restraints weight = 26065.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071348 restraints weight = 21435.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072144 restraints weight = 18865.831| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25602 Z= 0.227 Angle : 0.719 20.186 34998 Z= 0.341 Chirality : 0.048 0.603 4186 Planarity : 0.004 0.046 4381 Dihedral : 7.621 81.270 4938 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.68 % Favored : 93.29 % Rotamer: Outliers : 1.24 % Allowed : 14.84 % Favored : 83.93 % 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: -1.06 (0.15), residues: 3009 helix: 1.33 (0.21), residues: 685 sheet: -0.44 (0.20), residues: 661 loop : -1.77 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.016 0.001 TYR A 91 PHE 0.024 0.002 PHE B1121 TRP 0.011 0.002 TRP B 353 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00530 (25488) covalent geometry : angle 0.66601 (34691) SS BOND : bond 0.00446 ( 35) SS BOND : angle 1.55040 ( 70) hydrogen bonds : bond 0.05739 ( 886) hydrogen bonds : angle 4.91278 ( 2385) link_BETA1-4 : bond 0.00637 ( 32) link_BETA1-4 : angle 2.93104 ( 96) link_NAG-ASN : bond 0.00553 ( 47) link_NAG-ASN : angle 3.49795 ( 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 115 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9024 (tmm) cc_final: 0.7984 (tmm) REVERT: B 518 LEU cc_start: 0.8203 (mt) cc_final: 0.7971 (mp) REVERT: B 1002 GLN cc_start: 0.7835 (tm130) cc_final: 0.7504 (tm-30) REVERT: B 1029 MET cc_start: 0.9139 (tmm) cc_final: 0.8241 (tmm) REVERT: C 869 MET cc_start: 0.8834 (mmm) cc_final: 0.8535 (mmm) REVERT: C 1050 MET cc_start: 0.8683 (ptm) cc_final: 0.8431 (ptp) outliers start: 33 outliers final: 24 residues processed: 110 average time/residue: 0.1387 time to fit residues: 27.1395 Evaluate side-chains 103 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 543 PHE 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 638 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 102 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3843 r_free = 0.3843 target = 0.106836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067101 restraints weight = 63914.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069982 restraints weight = 35741.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071867 restraints weight = 25694.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073117 restraints weight = 20954.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073932 restraints weight = 18393.554| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.003 0.044 25602 Z= 0.133 Angle : 0.658 20.493 34998 Z= 0.306 Chirality : 0.046 0.585 4186 Planarity : 0.004 0.048 4381 Dihedral : 7.356 81.509 4938 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 1.12 % Allowed : 15.21 % Favored : 83.66 % 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: -0.96 (0.15), residues: 3009 helix: 1.45 (0.21), residues: 683 sheet: -0.35 (0.21), residues: 634 loop : -1.71 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.014 0.001 TYR B1067 PHE 0.013 0.001 PHE A1121 TRP 0.013 0.001 TRP B 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (25488) covalent geometry : angle 0.60050 (34691) SS BOND : bond 0.00379 ( 35) SS BOND : angle 1.52818 ( 70) hydrogen bonds : bond 0.05033 ( 886) hydrogen bonds : angle 4.74270 ( 2385) link_BETA1-4 : bond 0.00694 ( 32) link_BETA1-4 : angle 2.91328 ( 96) link_NAG-ASN : bond 0.00572 ( 47) link_NAG-ASN : angle 3.41937 ( 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 111 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8997 (tmm) cc_final: 0.8022 (tmm) REVERT: B 64 TRP cc_start: 0.8466 (t60) cc_final: 0.8051 (t60) REVERT: B 518 LEU cc_start: 0.8183 (mt) cc_final: 0.7952 (mp) REVERT: B 1002 GLN cc_start: 0.7752 (tm130) cc_final: 0.7381 (tm-30) REVERT: B 1029 MET cc_start: 0.9115 (tmm) cc_final: 0.8246 (tmm) REVERT: C 869 MET cc_start: 0.8768 (mmm) cc_final: 0.8520 (mmm) REVERT: C 872 GLN cc_start: 0.8520 (tp40) cc_final: 0.8307 (tp40) REVERT: C 918 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: C 1050 MET cc_start: 0.8638 (ptm) cc_final: 0.8376 (ptp) outliers start: 30 outliers final: 23 residues processed: 108 average time/residue: 0.1321 time to fit residues: 25.5393 Evaluate side-chains 104 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 543 PHE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 232 optimal weight: 0.6980 chunk 281 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 0.0770 chunk 249 optimal weight: 0.0470 chunk 101 optimal weight: 10.0000 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3870 r_free = 0.3870 target = 0.108605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068917 restraints weight = 63450.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071955 restraints weight = 34862.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073921 restraints weight = 24773.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075278 restraints weight = 20105.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.076128 restraints weight = 17526.311| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1741 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= 0.106 Angle : 0.628 20.700 34998 Z= 0.290 Chirality : 0.046 0.570 4186 Planarity : 0.004 0.049 4381 Dihedral : 7.105 82.760 4938 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 0.97 % Allowed : 15.32 % 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: -0.77 (0.15), residues: 3009 helix: 1.67 (0.21), residues: 672 sheet: -0.24 (0.21), residues: 620 loop : -1.59 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.015 0.001 TYR B1067 PHE 0.013 0.001 PHE B 456 TRP 0.012 0.001 TRP B 104 HIS 0.006 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00232 (25488) covalent geometry : angle 0.57101 (34691) SS BOND : bond 0.00330 ( 35) SS BOND : angle 1.24633 ( 70) hydrogen bonds : bond 0.04309 ( 886) hydrogen bonds : angle 4.53069 ( 2385) link_BETA1-4 : bond 0.00755 ( 32) link_BETA1-4 : angle 2.80966 ( 96) link_NAG-ASN : bond 0.00601 ( 47) link_NAG-ASN : angle 3.37516 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4818.30 seconds wall clock time: 83 minutes 43.27 seconds (5023.27 seconds total)