Starting phenix.real_space_refine on Mon Aug 25 21:18:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7asd_11892/08_2025/7asd_11892_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7asd_11892/08_2025/7asd_11892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7asd_11892/08_2025/7asd_11892_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7asd_11892/08_2025/7asd_11892_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7asd_11892/08_2025/7asd_11892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7asd_11892/08_2025/7asd_11892.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 144 5.16 5 C 19144 2.51 5 N 4960 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30296 Number of models: 1 Model: "" Number of chains: 48 Chain: "AA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "AB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "BA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "BB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "CA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "CB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "DA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "DB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "EA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "EB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "FA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "FB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "GA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "GB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "HA" Number of atoms: 3316 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} Conformer: "B" Number of residues, atoms: 413, 3296 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 396} bond proxies already assigned to first conformer: 3343 Chain: "HB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 327 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "AAc" 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: 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: "BAc" 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: 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: "CAc" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "DAc" 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: 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: "EAc" 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: 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: "FAc" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "GAc" 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: 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: "HAc" 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: 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: "AA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "AB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "BB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "CA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "CB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "DA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "DB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "EA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "EB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "FA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "FB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "GA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "GB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Chain: "HA" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'94R': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "HB" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'94R': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N AHISAA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISAA 172 " occ=0.50 residue: pdb=" N AHISAA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISAA 294 " occ=0.40 residue: pdb=" N AHISBA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISBA 172 " occ=0.50 residue: pdb=" N AHISBA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISBA 294 " occ=0.40 residue: pdb=" N AHISCA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISCA 172 " occ=0.50 residue: pdb=" N AHISCA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISCA 294 " occ=0.40 residue: pdb=" N AHISDA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISDA 172 " occ=0.50 residue: pdb=" N AHISDA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISDA 294 " occ=0.40 residue: pdb=" N AHISEA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISEA 172 " occ=0.50 residue: pdb=" N AHISEA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISEA 294 " occ=0.40 residue: pdb=" N AHISFA 172 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISFA 172 " occ=0.50 residue: pdb=" N AHISFA 294 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHISFA 294 " occ=0.40 ... (remaining 4 not shown) Time building chain proxies: 10.68, per 1000 atoms: 0.35 Number of scatterers: 30296 At special positions: 0 Unit cell: (149.334, 151.723, 127.83, 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 144 16.00 O 6048 8.00 N 4960 7.00 C 19144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYSAA 118 " - pdb=" SG CYSAA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 132 " - pdb=" SG CYSAA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 329 " - pdb=" SG CYSAA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 118 " - pdb=" SG CYSBA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 132 " - pdb=" SG CYSBA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 329 " - pdb=" SG CYSBA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 118 " - pdb=" SG CYSCA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 132 " - pdb=" SG CYSCA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 329 " - pdb=" SG CYSCA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 118 " - pdb=" SG CYSDA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 132 " - pdb=" SG CYSDA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 329 " - pdb=" SG CYSDA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 118 " - pdb=" SG CYSEA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 132 " - pdb=" SG CYSEA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 329 " - pdb=" SG CYSEA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 118 " - pdb=" SG CYSFA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 132 " - pdb=" SG CYSFA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 329 " - pdb=" SG CYSFA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSGA 118 " - pdb=" SG CYSGA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSGA 132 " - pdb=" SG CYSGA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSGA 329 " - pdb=" SG CYSGA 416 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 118 " - pdb=" SG CYSHA 150 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 132 " - pdb=" SG CYSHA 195 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 329 " - pdb=" SG CYSHA 416 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAGAAc 1 " - " NAGAAc 2 " " NAGBAc 1 " - " NAGBAc 2 " " NAGCAc 1 " - " NAGCAc 2 " " NAGDAc 1 " - " NAGDAc 2 " " NAGEAc 1 " - " NAGEAc 2 " " NAGFAc 1 " - " NAGFAc 2 " " NAGGAc 1 " - " NAGGAc 2 " " NAGHAc 1 " - " NAGHAc 2 " NAG-ASN " NAG A 1 " - " ASNAA 177 " " NAG B 1 " - " ASNBA 177 " " NAG C 1 " - " ASNCA 177 " " NAG D 1 " - " ASNDA 177 " " NAG E 1 " - " ASNEA 177 " " NAG F 1 " - " ASNFA 177 " " NAG G 1 " - " ASNGA 177 " " NAG H 1 " - " ASNHA 177 " " NAGAA 502 " - " ASNAA 28 " " NAGAAc 1 " - " ASNAA 144 " " NAGBA 502 " - " ASNBA 28 " " NAGBAc 1 " - " ASNBA 144 " " NAGCA 502 " - " ASNCA 28 " " NAGCAc 1 " - " ASNCA 144 " " NAGDA 502 " - " ASNDA 28 " " NAGDAc 1 " - " ASNDA 144 " " NAGEA 502 " - " ASNEA 28 " " NAGEAc 1 " - " ASNEA 144 " " NAGFA 502 " - " ASNFA 28 " " NAGFAc 1 " - " ASNFA 144 " " NAGGA 502 " - " ASNGA 28 " " NAGGAc 1 " - " ASNGA 144 " " NAGHA 502 " - " ASNHA 28 " " NAGHAc 1 " - " ASNHA 144 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 1.4 microseconds 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 68 sheets defined 19.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'AA' and resid 46 through 56 Processing helix chain 'AA' and resid 171 through 176 Processing helix chain 'AA' and resid 228 through 232 Processing helix chain 'AA' and resid 234 through 237 Processing helix chain 'AA' and resid 281 through 285 removed outlier: 3.907A pdb=" N THRAA 285 " --> pdb=" O GLNAA 282 " (cutoff:3.500A) Processing helix chain 'AA' and resid 367 through 371 removed outlier: 3.678A pdb=" N ASPAA 370 " --> pdb=" O PROAA 367 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGAA 371 " --> pdb=" O ILEAA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 367 through 371' Processing helix chain 'AA' and resid 384 through 391 Processing helix chain 'AA' and resid 407 through 411 Processing helix chain 'AB' and resid 34 through 52 Processing helix chain 'AB' and resid 56 through 74 Processing helix chain 'BA' and resid 46 through 56 Processing helix chain 'BA' and resid 171 through 176 Processing helix chain 'BA' and resid 228 through 232 Processing helix chain 'BA' and resid 234 through 237 Processing helix chain 'BA' and resid 281 through 285 removed outlier: 3.906A pdb=" N THRBA 285 " --> pdb=" O GLNBA 282 " (cutoff:3.500A) Processing helix chain 'BA' and resid 367 through 371 removed outlier: 3.678A pdb=" N ASPBA 370 " --> pdb=" O PROBA 367 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARGBA 371 " --> pdb=" O ILEBA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 367 through 371' Processing helix chain 'BA' and resid 384 through 391 Processing helix chain 'BA' and resid 407 through 411 Processing helix chain 'BB' and resid 34 through 52 Processing helix chain 'BB' and resid 56 through 74 Processing helix chain 'CA' and resid 46 through 56 Processing helix chain 'CA' and resid 171 through 176 Processing helix chain 'CA' and resid 228 through 232 Processing helix chain 'CA' and resid 234 through 237 Processing helix chain 'CA' and resid 281 through 285 removed outlier: 3.907A pdb=" N THRCA 285 " --> pdb=" O GLNCA 282 " (cutoff:3.500A) Processing helix chain 'CA' and resid 367 through 371 removed outlier: 3.679A pdb=" N ASPCA 370 " --> pdb=" O PROCA 367 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGCA 371 " --> pdb=" O ILECA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 367 through 371' Processing helix chain 'CA' and resid 384 through 391 Processing helix chain 'CA' and resid 407 through 411 Processing helix chain 'CB' and resid 34 through 52 Processing helix chain 'CB' and resid 56 through 74 Processing helix chain 'DA' and resid 46 through 56 Processing helix chain 'DA' and resid 171 through 176 Processing helix chain 'DA' and resid 228 through 232 Processing helix chain 'DA' and resid 234 through 237 Processing helix chain 'DA' and resid 281 through 284 Processing helix chain 'DA' and resid 367 through 371 removed outlier: 3.679A pdb=" N ASPDA 370 " --> pdb=" O PRODA 367 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARGDA 371 " --> pdb=" O ILEDA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 367 through 371' Processing helix chain 'DA' and resid 384 through 391 Processing helix chain 'DA' and resid 407 through 411 Processing helix chain 'DB' and resid 34 through 52 Processing helix chain 'DB' and resid 56 through 74 Processing helix chain 'EA' and resid 46 through 56 Processing helix chain 'EA' and resid 171 through 176 Processing helix chain 'EA' and resid 228 through 232 Processing helix chain 'EA' and resid 234 through 237 Processing helix chain 'EA' and resid 281 through 285 removed outlier: 3.907A pdb=" N THREA 285 " --> pdb=" O GLNEA 282 " (cutoff:3.500A) Processing helix chain 'EA' and resid 367 through 371 removed outlier: 3.679A pdb=" N ASPEA 370 " --> pdb=" O PROEA 367 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGEA 371 " --> pdb=" O ILEEA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'EA' and resid 367 through 371' Processing helix chain 'EA' and resid 384 through 391 Processing helix chain 'EA' and resid 407 through 411 Processing helix chain 'EB' and resid 34 through 52 Processing helix chain 'EB' and resid 56 through 74 Processing helix chain 'FA' and resid 46 through 56 Processing helix chain 'FA' and resid 171 through 176 Processing helix chain 'FA' and resid 228 through 232 Processing helix chain 'FA' and resid 234 through 237 Processing helix chain 'FA' and resid 281 through 285 removed outlier: 3.907A pdb=" N THRFA 285 " --> pdb=" O GLNFA 282 " (cutoff:3.500A) Processing helix chain 'FA' and resid 367 through 371 removed outlier: 3.678A pdb=" N ASPFA 370 " --> pdb=" O PROFA 367 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGFA 371 " --> pdb=" O ILEFA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 367 through 371' Processing helix chain 'FA' and resid 384 through 391 Processing helix chain 'FA' and resid 407 through 411 Processing helix chain 'FB' and resid 34 through 52 Processing helix chain 'FB' and resid 56 through 74 Processing helix chain 'GA' and resid 46 through 56 Processing helix chain 'GA' and resid 171 through 176 Processing helix chain 'GA' and resid 228 through 232 Processing helix chain 'GA' and resid 234 through 237 Processing helix chain 'GA' and resid 281 through 285 removed outlier: 3.907A pdb=" N THRGA 285 " --> pdb=" O GLNGA 282 " (cutoff:3.500A) Processing helix chain 'GA' and resid 367 through 371 removed outlier: 3.679A pdb=" N ASPGA 370 " --> pdb=" O PROGA 367 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGGA 371 " --> pdb=" O ILEGA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'GA' and resid 367 through 371' Processing helix chain 'GA' and resid 384 through 391 Processing helix chain 'GA' and resid 407 through 411 Processing helix chain 'GB' and resid 34 through 52 Processing helix chain 'GB' and resid 56 through 74 Processing helix chain 'HA' and resid 46 through 56 Processing helix chain 'HA' and resid 171 through 176 Processing helix chain 'HA' and resid 228 through 232 Processing helix chain 'HA' and resid 234 through 237 Processing helix chain 'HA' and resid 281 through 285 removed outlier: 3.906A pdb=" N THRHA 285 " --> pdb=" O GLNHA 282 " (cutoff:3.500A) Processing helix chain 'HA' and resid 367 through 371 removed outlier: 3.678A pdb=" N ASPHA 370 " --> pdb=" O PROHA 367 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGHA 371 " --> pdb=" O ILEHA 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'HA' and resid 367 through 371' Processing helix chain 'HA' and resid 384 through 391 Processing helix chain 'HA' and resid 407 through 411 Processing helix chain 'HB' and resid 34 through 52 Processing helix chain 'HB' and resid 56 through 74 Processing sheet with id=AA1, first strand: chain 'AA' and resid 33 through 37 removed outlier: 5.567A pdb=" N ILEAA 33 " --> pdb=" O ASNAA 404 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASNAA 404 " --> pdb=" O ILEAA 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HISAA 35 " --> pdb=" O ILEAA 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERAA 356 " --> pdb=" O LEUAA 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 66 through 72 removed outlier: 6.490A pdb=" N THRAA 79 " --> pdb=" O SERAA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILEAA 69 " --> pdb=" O PHEAA 77 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHEAA 77 " --> pdb=" O ILEAA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNAA 71 " --> pdb=" O LYSAA 75 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYSAA 75 " --> pdb=" O GLNAA 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILEAA 76 " --> pdb=" O ILEAA 93 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEUAA 103 " --> pdb=" O SERAA 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSAA 126 " --> pdb=" O LEUAA 138 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASPAA 158 " --> pdb=" O LEUAA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUAA 164 " --> pdb=" O ASPAA 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AA' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'AA' and resid 185 through 194 removed outlier: 7.196A pdb=" N ASPAA 200 " --> pdb=" O LEUAA 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AA' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'AA' and resid 253 through 258 removed outlier: 5.477A pdb=" N GLYAA 255 " --> pdb=" O SERAA 268 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SERAA 268 " --> pdb=" O GLYAA 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AA' and resid 306 through 311 removed outlier: 4.845A pdb=" N ALAAA 308 " --> pdb=" O GLYAA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUAA 327 " --> pdb=" O VALAA 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AA' and resid 373 through 374 Processing sheet with id=AB1, first strand: chain 'BA' and resid 33 through 37 removed outlier: 5.567A pdb=" N ILEBA 33 " --> pdb=" O ASNBA 404 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASNBA 404 " --> pdb=" O ILEBA 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HISBA 35 " --> pdb=" O ILEBA 402 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SERBA 356 " --> pdb=" O LEUBA 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'BA' and resid 66 through 72 removed outlier: 6.491A pdb=" N THRBA 79 " --> pdb=" O SERBA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILEBA 69 " --> pdb=" O PHEBA 77 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHEBA 77 " --> pdb=" O ILEBA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNBA 71 " --> pdb=" O LYSBA 75 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYSBA 75 " --> pdb=" O GLNBA 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILEBA 76 " --> pdb=" O ILEBA 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEUBA 103 " --> pdb=" O SERBA 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'BA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSBA 126 " --> pdb=" O LEUBA 138 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASPBA 158 " --> pdb=" O LEUBA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUBA 164 " --> pdb=" O ASPBA 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'BA' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'BA' and resid 185 through 194 removed outlier: 7.196A pdb=" N ASPBA 200 " --> pdb=" O LEUBA 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'BA' and resid 239 through 242 Processing sheet with id=AB7, first strand: chain 'BA' and resid 253 through 258 removed outlier: 5.476A pdb=" N GLYBA 255 " --> pdb=" O SERBA 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SERBA 268 " --> pdb=" O GLYBA 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'BA' and resid 306 through 311 removed outlier: 4.845A pdb=" N ALABA 308 " --> pdb=" O GLYBA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUBA 327 " --> pdb=" O VALBA 344 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'CA' and resid 33 through 37 removed outlier: 5.566A pdb=" N ILECA 33 " --> pdb=" O ASNCA 404 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASNCA 404 " --> pdb=" O ILECA 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HISCA 35 " --> pdb=" O ILECA 402 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SERCA 356 " --> pdb=" O LEUCA 381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'CA' and resid 66 through 72 removed outlier: 6.490A pdb=" N THRCA 79 " --> pdb=" O SERCA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILECA 69 " --> pdb=" O PHECA 77 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHECA 77 " --> pdb=" O ILECA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNCA 71 " --> pdb=" O LYSCA 75 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYSCA 75 " --> pdb=" O GLNCA 71 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILECA 76 " --> pdb=" O ILECA 93 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEUCA 103 " --> pdb=" O SERCA 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'CA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSCA 126 " --> pdb=" O LEUCA 138 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASPCA 158 " --> pdb=" O LEUCA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUCA 164 " --> pdb=" O ASPCA 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'CA' and resid 142 through 143 Processing sheet with id=AC4, first strand: chain 'CA' and resid 185 through 194 removed outlier: 7.197A pdb=" N ASPCA 200 " --> pdb=" O LEUCA 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'CA' and resid 239 through 242 Processing sheet with id=AC6, first strand: chain 'CA' and resid 253 through 258 removed outlier: 5.476A pdb=" N GLYCA 255 " --> pdb=" O SERCA 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SERCA 268 " --> pdb=" O GLYCA 255 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'CA' and resid 306 through 311 removed outlier: 4.845A pdb=" N ALACA 308 " --> pdb=" O GLYCA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUCA 327 " --> pdb=" O VALCA 344 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'CA' and resid 373 through 374 Processing sheet with id=AC9, first strand: chain 'DA' and resid 33 through 37 removed outlier: 5.566A pdb=" N ILEDA 33 " --> pdb=" O ASNDA 404 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASNDA 404 " --> pdb=" O ILEDA 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HISDA 35 " --> pdb=" O ILEDA 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERDA 356 " --> pdb=" O LEUDA 381 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'DA' and resid 66 through 72 removed outlier: 6.491A pdb=" N THRDA 79 " --> pdb=" O SERDA 67 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILEDA 69 " --> pdb=" O PHEDA 77 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHEDA 77 " --> pdb=" O ILEDA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNDA 71 " --> pdb=" O LYSDA 75 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYSDA 75 " --> pdb=" O GLNDA 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILEDA 76 " --> pdb=" O ILEDA 93 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEUDA 103 " --> pdb=" O SERDA 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'DA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSDA 126 " --> pdb=" O LEUDA 138 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASPDA 158 " --> pdb=" O LEUDA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUDA 164 " --> pdb=" O ASPDA 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'DA' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'DA' and resid 185 through 194 removed outlier: 7.196A pdb=" N ASPDA 200 " --> pdb=" O LEUDA 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'DA' and resid 239 through 242 Processing sheet with id=AD6, first strand: chain 'DA' and resid 253 through 258 removed outlier: 5.476A pdb=" N GLYDA 255 " --> pdb=" O SERDA 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SERDA 268 " --> pdb=" O GLYDA 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'DA' and resid 306 through 311 removed outlier: 4.846A pdb=" N ALADA 308 " --> pdb=" O GLYDA 320 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEUDA 327 " --> pdb=" O VALDA 344 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'EA' and resid 33 through 37 removed outlier: 5.566A pdb=" N ILEEA 33 " --> pdb=" O ASNEA 404 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASNEA 404 " --> pdb=" O ILEEA 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HISEA 35 " --> pdb=" O ILEEA 402 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SEREA 356 " --> pdb=" O LEUEA 381 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'EA' and resid 66 through 72 removed outlier: 6.490A pdb=" N THREA 79 " --> pdb=" O SEREA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILEEA 69 " --> pdb=" O PHEEA 77 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHEEA 77 " --> pdb=" O ILEEA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNEA 71 " --> pdb=" O LYSEA 75 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYSEA 75 " --> pdb=" O GLNEA 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILEEA 76 " --> pdb=" O ILEEA 93 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEUEA 103 " --> pdb=" O SEREA 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'EA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSEA 126 " --> pdb=" O LEUEA 138 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASPEA 158 " --> pdb=" O LEUEA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUEA 164 " --> pdb=" O ASPEA 158 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'EA' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'EA' and resid 185 through 194 removed outlier: 7.196A pdb=" N ASPEA 200 " --> pdb=" O LEUEA 193 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'EA' and resid 239 through 242 Processing sheet with id=AE5, first strand: chain 'EA' and resid 253 through 258 removed outlier: 5.477A pdb=" N GLYEA 255 " --> pdb=" O SEREA 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SEREA 268 " --> pdb=" O GLYEA 255 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'EA' and resid 306 through 311 removed outlier: 4.846A pdb=" N ALAEA 308 " --> pdb=" O GLYEA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUEA 327 " --> pdb=" O VALEA 344 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'EA' and resid 373 through 374 Processing sheet with id=AE8, first strand: chain 'FA' and resid 33 through 37 removed outlier: 5.566A pdb=" N ILEFA 33 " --> pdb=" O ASNFA 404 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASNFA 404 " --> pdb=" O ILEFA 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HISFA 35 " --> pdb=" O ILEFA 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERFA 356 " --> pdb=" O LEUFA 381 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'FA' and resid 66 through 72 removed outlier: 6.490A pdb=" N THRFA 79 " --> pdb=" O SERFA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILEFA 69 " --> pdb=" O PHEFA 77 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHEFA 77 " --> pdb=" O ILEFA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNFA 71 " --> pdb=" O LYSFA 75 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYSFA 75 " --> pdb=" O GLNFA 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILEFA 76 " --> pdb=" O ILEFA 93 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEUFA 103 " --> pdb=" O SERFA 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'FA' and resid 124 through 129 removed outlier: 4.124A pdb=" N LYSFA 126 " --> pdb=" O LEUFA 138 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASPFA 158 " --> pdb=" O LEUFA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUFA 164 " --> pdb=" O ASPFA 158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'FA' and resid 142 through 143 Processing sheet with id=AF3, first strand: chain 'FA' and resid 185 through 194 removed outlier: 7.196A pdb=" N ASPFA 200 " --> pdb=" O LEUFA 193 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'FA' and resid 239 through 242 Processing sheet with id=AF5, first strand: chain 'FA' and resid 253 through 258 removed outlier: 5.476A pdb=" N GLYFA 255 " --> pdb=" O SERFA 268 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SERFA 268 " --> pdb=" O GLYFA 255 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'FA' and resid 306 through 311 removed outlier: 4.845A pdb=" N ALAFA 308 " --> pdb=" O GLYFA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUFA 327 " --> pdb=" O VALFA 344 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'GA' and resid 33 through 37 removed outlier: 5.566A pdb=" N ILEGA 33 " --> pdb=" O ASNGA 404 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASNGA 404 " --> pdb=" O ILEGA 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HISGA 35 " --> pdb=" O ILEGA 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERGA 356 " --> pdb=" O LEUGA 381 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'GA' and resid 66 through 72 removed outlier: 6.491A pdb=" N THRGA 79 " --> pdb=" O SERGA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILEGA 69 " --> pdb=" O PHEGA 77 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHEGA 77 " --> pdb=" O ILEGA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNGA 71 " --> pdb=" O LYSGA 75 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYSGA 75 " --> pdb=" O GLNGA 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILEGA 76 " --> pdb=" O ILEGA 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEUGA 103 " --> pdb=" O SERGA 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'GA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSGA 126 " --> pdb=" O LEUGA 138 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASPGA 158 " --> pdb=" O LEUGA 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEUGA 164 " --> pdb=" O ASPGA 158 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'GA' and resid 142 through 143 Processing sheet with id=AG2, first strand: chain 'GA' and resid 185 through 194 removed outlier: 7.196A pdb=" N ASPGA 200 " --> pdb=" O LEUGA 193 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'GA' and resid 239 through 242 Processing sheet with id=AG4, first strand: chain 'GA' and resid 253 through 258 removed outlier: 5.477A pdb=" N GLYGA 255 " --> pdb=" O SERGA 268 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SERGA 268 " --> pdb=" O GLYGA 255 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'GA' and resid 306 through 311 removed outlier: 4.845A pdb=" N ALAGA 308 " --> pdb=" O GLYGA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUGA 327 " --> pdb=" O VALGA 344 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'GA' and resid 373 through 374 Processing sheet with id=AG7, first strand: chain 'HA' and resid 33 through 37 removed outlier: 5.566A pdb=" N ILEHA 33 " --> pdb=" O ASNHA 404 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASNHA 404 " --> pdb=" O ILEHA 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HISHA 35 " --> pdb=" O ILEHA 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SERHA 356 " --> pdb=" O LEUHA 381 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'HA' and resid 66 through 72 removed outlier: 6.491A pdb=" N THRHA 79 " --> pdb=" O SERHA 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILEHA 69 " --> pdb=" O PHEHA 77 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHEHA 77 " --> pdb=" O ILEHA 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLNHA 71 " --> pdb=" O LYSHA 75 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYSHA 75 " --> pdb=" O GLNHA 71 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILEHA 76 " --> pdb=" O ILEHA 93 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEUHA 103 " --> pdb=" O SERHA 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'HA' and resid 124 through 129 removed outlier: 4.125A pdb=" N LYSHA 126 " --> pdb=" O LEUHA 138 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASPHA 158 " --> pdb=" O LEUHA 164 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUHA 164 " --> pdb=" O ASPHA 158 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'HA' and resid 142 through 143 Processing sheet with id=AH2, first strand: chain 'HA' and resid 185 through 194 removed outlier: 7.197A pdb=" N ASPHA 200 " --> pdb=" O LEUHA 193 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'HA' and resid 239 through 242 Processing sheet with id=AH4, first strand: chain 'HA' and resid 253 through 258 removed outlier: 5.475A pdb=" N GLYHA 255 " --> pdb=" O SERHA 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SERHA 268 " --> pdb=" O GLYHA 255 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'HA' and resid 306 through 311 removed outlier: 4.845A pdb=" N ALAHA 308 " --> pdb=" O GLYHA 320 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEUHA 327 " --> pdb=" O VALHA 344 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 2880 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: 5.65 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9864 1.35 - 1.47: 7159 1.47 - 1.58: 13689 1.58 - 1.70: 0 1.70 - 1.82: 224 Bond restraints: 30936 Sorted by residual: bond pdb=" O3 SO4FA 503 " pdb=" S SO4FA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" O3 SO4GA 503 " pdb=" S SO4GA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" O3 SO4HA 503 " pdb=" S SO4HA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" O4 SO4AA 503 " pdb=" S SO4AA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" O4 SO4BA 503 " pdb=" S SO4BA 503 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 30931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 40877 1.70 - 3.39: 1028 3.39 - 5.09: 197 5.09 - 6.79: 26 6.79 - 8.48: 32 Bond angle restraints: 42160 Sorted by residual: angle pdb=" C ASNBA 196 " pdb=" N THRBA 197 " pdb=" CA THRBA 197 " ideal model delta sigma weight residual 120.82 125.76 -4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C ASNAA 196 " pdb=" N THRAA 197 " pdb=" CA THRAA 197 " ideal model delta sigma weight residual 120.82 125.75 -4.93 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C ASNCA 196 " pdb=" N THRCA 197 " pdb=" CA THRCA 197 " ideal model delta sigma weight residual 120.82 125.75 -4.93 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C ASNFA 196 " pdb=" N THRFA 197 " pdb=" CA THRFA 197 " ideal model delta sigma weight residual 120.82 125.73 -4.91 1.50e+00 4.44e-01 1.07e+01 angle pdb=" C ASNEA 196 " pdb=" N THREA 197 " pdb=" CA THREA 197 " ideal model delta sigma weight residual 120.82 125.70 -4.88 1.50e+00 4.44e-01 1.06e+01 ... (remaining 42155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 19246 21.61 - 43.21: 586 43.21 - 64.82: 72 64.82 - 86.43: 48 86.43 - 108.03: 32 Dihedral angle restraints: 19984 sinusoidal: 9144 harmonic: 10840 Sorted by residual: dihedral pdb=" CB CYSEA 132 " pdb=" SG CYSEA 132 " pdb=" SG CYSEA 195 " pdb=" CB CYSEA 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.06 45.06 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYSGA 132 " pdb=" SG CYSGA 132 " pdb=" SG CYSGA 195 " pdb=" CB CYSGA 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.04 45.04 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYSBA 132 " pdb=" SG CYSBA 132 " pdb=" SG CYSBA 195 " pdb=" CB CYSBA 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.04 45.04 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 19981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4699 0.105 - 0.210: 189 0.210 - 0.316: 40 0.316 - 0.421: 0 0.421 - 0.526: 16 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C14 94RFA 501 " pdb=" C13 94RFA 501 " pdb=" C15 94RFA 501 " pdb=" C8 94RFA 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" C14 94RBA 501 " pdb=" C13 94RBA 501 " pdb=" C15 94RBA 501 " pdb=" C8 94RBA 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C14 94RAA 501 " pdb=" C13 94RAA 501 " pdb=" C15 94RAA 501 " pdb=" C8 94RAA 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.52 2.00e-01 2.50e+01 6.89e+00 ... (remaining 4941 not shown) Planarity restraints: 5360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRPHA 72 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C TRPHA 72 " 0.023 2.00e-02 2.50e+03 pdb=" O TRPHA 72 " -0.009 2.00e-02 2.50e+03 pdb=" N HISHA 73 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPGA 72 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C TRPGA 72 " -0.023 2.00e-02 2.50e+03 pdb=" O TRPGA 72 " 0.009 2.00e-02 2.50e+03 pdb=" N HISGA 73 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPEA 72 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C TRPEA 72 " 0.023 2.00e-02 2.50e+03 pdb=" O TRPEA 72 " -0.009 2.00e-02 2.50e+03 pdb=" N HISEA 73 " -0.008 2.00e-02 2.50e+03 ... (remaining 5357 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 812 2.70 - 3.25: 29191 3.25 - 3.80: 45983 3.80 - 4.35: 62770 4.35 - 4.90: 105608 Nonbonded interactions: 244364 Sorted by model distance: nonbonded pdb=" OG SERGA 325 " pdb=" O LEUGA 351 " model vdw 2.153 3.040 nonbonded pdb=" OG SEREA 325 " pdb=" O LEUEA 351 " model vdw 2.153 3.040 nonbonded pdb=" OG SERCA 325 " pdb=" O LEUCA 351 " model vdw 2.153 3.040 nonbonded pdb=" OG SERDA 325 " pdb=" O LEUDA 351 " model vdw 2.153 3.040 nonbonded pdb=" OG SERAA 325 " pdb=" O LEUAA 351 " model vdw 2.154 3.040 ... (remaining 244359 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: 0.11 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'GA' selection = chain 'HA' } ncs_group { reference = chain 'AB' selection = chain 'BB' selection = chain 'CB' selection = chain 'DB' selection = chain 'EB' selection = chain 'FB' selection = chain 'GB' selection = chain 'HB' } ncs_group { reference = chain 'AAc' selection = chain 'BAc' selection = chain 'CAc' selection = chain 'DAc' selection = chain 'EAc' selection = chain 'FAc' selection = chain 'GAc' selection = chain 'HAc' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.99 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.003 0.040 31008 Z= 0.178 Angle : 0.688 8.482 42352 Z= 0.355 Chirality : 0.059 0.526 4944 Planarity : 0.003 0.029 5336 Dihedral : 11.932 108.032 12904 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 4.56 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: 0.30 (0.14), residues: 3680 helix: 1.46 (0.22), residues: 680 sheet: 1.17 (0.16), residues: 1056 loop : -0.85 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGHA 415 TYR 0.008 0.001 TYRHA 377 PHE 0.009 0.001 PHEFA 157 TRP 0.008 0.001 TRPDA 72 HIS 0.002 0.001 HISGA 217 Details of bonding type rmsd covalent geometry : bond 0.00339 (30936) covalent geometry : angle 0.68449 (42160) SS BOND : bond 0.00129 ( 24) SS BOND : angle 0.92457 ( 48) hydrogen bonds : bond 0.18777 ( 1072) hydrogen bonds : angle 5.88203 ( 2880) link_BETA1-4 : bond 0.00246 ( 24) link_BETA1-4 : angle 1.44962 ( 72) link_NAG-ASN : bond 0.00143 ( 24) link_NAG-ASN : angle 1.20717 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 349 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 202 MET cc_start: 0.7514 (mtp) cc_final: 0.6451 (mtm) REVERT: AB 56 SER cc_start: 0.9257 (t) cc_final: 0.8980 (p) REVERT: BA 202 MET cc_start: 0.7444 (mtp) cc_final: 0.6962 (mtp) REVERT: BA 242 ILE cc_start: 0.7837 (mt) cc_final: 0.7297 (mt) REVERT: BA 353 MET cc_start: 0.8262 (tpt) cc_final: 0.8003 (tpt) REVERT: BB 68 LEU cc_start: 0.9064 (mt) cc_final: 0.8753 (mt) REVERT: CA 202 MET cc_start: 0.7489 (mtp) cc_final: 0.7033 (mtp) REVERT: DA 261 MET cc_start: 0.7755 (ttp) cc_final: 0.7327 (ttm) REVERT: DB 56 SER cc_start: 0.9014 (t) cc_final: 0.8628 (p) REVERT: EA 202 MET cc_start: 0.7454 (mtp) cc_final: 0.6972 (mtp) REVERT: FA 207 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6781 (p0) REVERT: FB 56 SER cc_start: 0.9164 (t) cc_final: 0.8886 (p) REVERT: GA 301 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7992 (tt) REVERT: GB 56 SER cc_start: 0.9131 (t) cc_final: 0.8761 (p) REVERT: HA 242 ILE cc_start: 0.7879 (mt) cc_final: 0.7327 (mt) REVERT: HA 353 MET cc_start: 0.8310 (tpt) cc_final: 0.8054 (tpt) REVERT: HA 361 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7273 (mt-10) outliers start: 72 outliers final: 8 residues processed: 418 average time/residue: 0.1616 time to fit residues: 113.3231 Evaluate side-chains 191 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 207 ASP Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DA residue 207 ASP Chi-restraints excluded: chain EA residue 207 ASP Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FA residue 207 ASP Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 207 ASP Chi-restraints excluded: chain GA residue 301 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068224 restraints weight = 269440.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073248 restraints weight = 95069.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073297 restraints weight = 51787.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074280 restraints weight = 41895.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.076596 restraints weight = 36649.393| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 31008 Z= 0.348 Angle : 0.762 7.546 42352 Z= 0.384 Chirality : 0.049 0.191 4944 Planarity : 0.005 0.069 5336 Dihedral : 9.469 59.788 6016 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.62 % Allowed : 7.13 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.17 (0.14), residues: 3680 helix: 0.97 (0.21), residues: 696 sheet: 0.71 (0.15), residues: 1088 loop : -1.04 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGEA 284 TYR 0.021 0.003 TYRHA 276 PHE 0.025 0.003 PHECA 231 TRP 0.016 0.003 TRPEA 37 HIS 0.010 0.002 HISGA 217 Details of bonding type rmsd covalent geometry : bond 0.00813 (30936) covalent geometry : angle 0.74661 (42160) SS BOND : bond 0.02139 ( 24) SS BOND : angle 2.56722 ( 48) hydrogen bonds : bond 0.05792 ( 1072) hydrogen bonds : angle 5.49290 ( 2880) link_BETA1-4 : bond 0.00379 ( 24) link_BETA1-4 : angle 2.91086 ( 72) link_NAG-ASN : bond 0.00483 ( 24) link_NAG-ASN : angle 1.59261 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.791 Fit side-chains REVERT: AA 68 ASP cc_start: 0.7273 (t0) cc_final: 0.7038 (p0) REVERT: AB 56 SER cc_start: 0.9028 (t) cc_final: 0.8585 (p) REVERT: BA 202 MET cc_start: 0.6859 (mtp) cc_final: 0.5614 (mtp) REVERT: BA 284 ARG cc_start: 0.6514 (mmm160) cc_final: 0.5633 (mmm160) REVERT: BA 307 SER cc_start: 0.8580 (p) cc_final: 0.8370 (t) REVERT: BA 353 MET cc_start: 0.8320 (tpt) cc_final: 0.7912 (tpt) REVERT: DB 56 SER cc_start: 0.8935 (t) cc_final: 0.8476 (p) REVERT: EA 149 MET cc_start: 0.7757 (tmm) cc_final: 0.7458 (tmm) REVERT: FA 80 MET cc_start: 0.8881 (tpp) cc_final: 0.8445 (mmp) REVERT: FB 56 SER cc_start: 0.9023 (t) cc_final: 0.8578 (p) REVERT: GA 80 MET cc_start: 0.8885 (mmm) cc_final: 0.8670 (mmm) REVERT: GB 56 SER cc_start: 0.8951 (t) cc_final: 0.8497 (p) REVERT: HA 353 MET cc_start: 0.8288 (tpt) cc_final: 0.7945 (tpt) outliers start: 54 outliers final: 41 residues processed: 223 average time/residue: 0.1602 time to fit residues: 61.7317 Evaluate side-chains 201 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 132 CYS Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 256 MET Chi-restraints excluded: chain AB residue 38 VAL Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 125 SER Chi-restraints excluded: chain BB residue 71 LEU Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 69 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DB residue 38 VAL Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain FA residue 69 ILE Chi-restraints excluded: chain FA residue 89 SER Chi-restraints excluded: chain FA residue 132 CYS Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 38 VAL Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 69 ILE Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 132 CYS Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GB residue 38 VAL Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HB residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 13 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 231 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 344 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068330 restraints weight = 272130.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072632 restraints weight = 77706.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075583 restraints weight = 41536.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077451 restraints weight = 28684.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078646 restraints weight = 22796.950| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31008 Z= 0.104 Angle : 0.533 6.498 42352 Z= 0.273 Chirality : 0.042 0.190 4944 Planarity : 0.003 0.037 5336 Dihedral : 7.387 57.909 6004 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.66 % Allowed : 8.57 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: 0.08 (0.14), residues: 3680 helix: 1.49 (0.21), residues: 696 sheet: 0.81 (0.15), residues: 1072 loop : -0.97 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGHA 284 TYR 0.010 0.001 TYRHA 377 PHE 0.011 0.001 PHEHA 157 TRP 0.015 0.001 TRPEA 37 HIS 0.003 0.001 HISGA 224 Details of bonding type rmsd covalent geometry : bond 0.00222 (30936) covalent geometry : angle 0.52020 (42160) SS BOND : bond 0.00230 ( 24) SS BOND : angle 1.55979 ( 48) hydrogen bonds : bond 0.03748 ( 1072) hydrogen bonds : angle 4.94686 ( 2880) link_BETA1-4 : bond 0.00493 ( 24) link_BETA1-4 : angle 2.37213 ( 72) link_NAG-ASN : bond 0.00434 ( 24) link_NAG-ASN : angle 1.15693 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.212 Fit side-chains REVERT: AB 56 SER cc_start: 0.8889 (t) cc_final: 0.8402 (p) REVERT: BA 202 MET cc_start: 0.7042 (mtp) cc_final: 0.6246 (mtp) REVERT: BA 284 ARG cc_start: 0.6650 (mmm160) cc_final: 0.6347 (mmm160) REVERT: BA 353 MET cc_start: 0.8376 (tpt) cc_final: 0.7963 (tpt) REVERT: CA 202 MET cc_start: 0.7407 (mtp) cc_final: 0.6970 (mtp) REVERT: DA 80 MET cc_start: 0.8614 (mmm) cc_final: 0.8347 (mmm) REVERT: DA 261 MET cc_start: 0.7824 (ttp) cc_final: 0.7436 (ttm) REVERT: DA 403 MET cc_start: 0.8539 (mtm) cc_final: 0.8296 (mtm) REVERT: DB 56 SER cc_start: 0.8879 (t) cc_final: 0.8300 (p) REVERT: EA 149 MET cc_start: 0.7611 (tmm) cc_final: 0.7245 (tmm) REVERT: FB 56 SER cc_start: 0.8830 (t) cc_final: 0.8299 (p) REVERT: GA 403 MET cc_start: 0.8559 (mtm) cc_final: 0.8309 (mtm) REVERT: GB 56 SER cc_start: 0.8902 (t) cc_final: 0.8315 (p) REVERT: HA 284 ARG cc_start: 0.6856 (mmm160) cc_final: 0.6469 (mmm160) REVERT: HA 353 MET cc_start: 0.8359 (tpt) cc_final: 0.7967 (tpt) outliers start: 22 outliers final: 20 residues processed: 206 average time/residue: 0.1614 time to fit residues: 57.9296 Evaluate side-chains 191 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 253 ILE Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 185 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 300 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065501 restraints weight = 281091.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069643 restraints weight = 79089.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072474 restraints weight = 42413.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.074265 restraints weight = 29527.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075384 restraints weight = 23632.018| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31008 Z= 0.232 Angle : 0.603 6.271 42352 Z= 0.309 Chirality : 0.044 0.192 4944 Planarity : 0.003 0.047 5336 Dihedral : 7.023 50.614 6000 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.23 % Allowed : 8.60 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.08 (0.14), residues: 3680 helix: 1.37 (0.21), residues: 696 sheet: 0.61 (0.15), residues: 1088 loop : -1.01 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGHA 82 TYR 0.014 0.002 TYRFA 277 PHE 0.014 0.002 PHEBA 157 TRP 0.012 0.002 TRPEA 37 HIS 0.005 0.001 HISDA 217 Details of bonding type rmsd covalent geometry : bond 0.00542 (30936) covalent geometry : angle 0.58947 (42160) SS BOND : bond 0.00248 ( 24) SS BOND : angle 1.19392 ( 48) hydrogen bonds : bond 0.04663 ( 1072) hydrogen bonds : angle 5.12772 ( 2880) link_BETA1-4 : bond 0.00397 ( 24) link_BETA1-4 : angle 2.72653 ( 72) link_NAG-ASN : bond 0.00220 ( 24) link_NAG-ASN : angle 1.33264 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.123 Fit side-chains REVERT: AA 80 MET cc_start: 0.8996 (mmt) cc_final: 0.8475 (mmm) REVERT: AB 56 SER cc_start: 0.8944 (t) cc_final: 0.8429 (p) REVERT: BA 202 MET cc_start: 0.7280 (mtp) cc_final: 0.6592 (mtp) REVERT: BA 284 ARG cc_start: 0.6652 (mmm160) cc_final: 0.6339 (mmm160) REVERT: BA 307 SER cc_start: 0.8663 (p) cc_final: 0.8425 (t) REVERT: BA 353 MET cc_start: 0.8360 (tpt) cc_final: 0.7816 (tpt) REVERT: DA 403 MET cc_start: 0.8500 (mtm) cc_final: 0.8256 (mtm) REVERT: DB 56 SER cc_start: 0.8874 (t) cc_final: 0.8366 (p) REVERT: FB 56 SER cc_start: 0.8901 (t) cc_final: 0.8403 (p) REVERT: GA 403 MET cc_start: 0.8531 (mtm) cc_final: 0.8279 (mtm) REVERT: GB 56 SER cc_start: 0.8883 (t) cc_final: 0.8361 (p) REVERT: HA 353 MET cc_start: 0.8361 (tpt) cc_final: 0.7840 (tpt) outliers start: 41 outliers final: 36 residues processed: 203 average time/residue: 0.1572 time to fit residues: 56.0682 Evaluate side-chains 198 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 253 ILE Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CA residue 430 ILE Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HA residue 430 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 190 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066797 restraints weight = 252300.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070931 restraints weight = 75272.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073731 restraints weight = 40975.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075511 restraints weight = 28637.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076628 restraints weight = 22969.228| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31008 Z= 0.148 Angle : 0.538 9.451 42352 Z= 0.277 Chirality : 0.042 0.190 4944 Planarity : 0.003 0.050 5336 Dihedral : 6.566 52.368 6000 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.32 % Allowed : 9.14 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.04 (0.14), residues: 3680 helix: 1.51 (0.21), residues: 696 sheet: 0.56 (0.15), residues: 1088 loop : -0.98 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGFA 284 TYR 0.011 0.001 TYRGA 276 PHE 0.010 0.001 PHEHA 157 TRP 0.013 0.001 TRPBA 37 HIS 0.003 0.001 HISGA 224 Details of bonding type rmsd covalent geometry : bond 0.00339 (30936) covalent geometry : angle 0.52724 (42160) SS BOND : bond 0.00128 ( 24) SS BOND : angle 1.01160 ( 48) hydrogen bonds : bond 0.03866 ( 1072) hydrogen bonds : angle 4.97357 ( 2880) link_BETA1-4 : bond 0.00383 ( 24) link_BETA1-4 : angle 2.25955 ( 72) link_NAG-ASN : bond 0.00247 ( 24) link_NAG-ASN : angle 1.23285 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.129 Fit side-chains REVERT: AA 80 MET cc_start: 0.9051 (mmt) cc_final: 0.8821 (mmt) REVERT: AB 56 SER cc_start: 0.8879 (t) cc_final: 0.8350 (p) REVERT: BA 202 MET cc_start: 0.7234 (mtp) cc_final: 0.6612 (mtp) REVERT: BA 284 ARG cc_start: 0.6776 (mmm160) cc_final: 0.6467 (mmm160) REVERT: BA 353 MET cc_start: 0.8362 (tpt) cc_final: 0.7789 (tpt) REVERT: BB 73 ASP cc_start: 0.8126 (t0) cc_final: 0.7916 (t0) REVERT: CA 80 MET cc_start: 0.7720 (mmm) cc_final: 0.7495 (mmm) REVERT: DA 403 MET cc_start: 0.8457 (mtm) cc_final: 0.8204 (mtm) REVERT: DB 56 SER cc_start: 0.8935 (t) cc_final: 0.8346 (p) REVERT: EA 80 MET cc_start: 0.7802 (mmm) cc_final: 0.7576 (mmm) REVERT: FB 56 SER cc_start: 0.8972 (t) cc_final: 0.8393 (p) REVERT: GA 403 MET cc_start: 0.8517 (mtm) cc_final: 0.8265 (mtm) REVERT: GB 56 SER cc_start: 0.8952 (t) cc_final: 0.8358 (p) REVERT: HA 353 MET cc_start: 0.8373 (tpt) cc_final: 0.7861 (tpt) outliers start: 44 outliers final: 37 residues processed: 199 average time/residue: 0.1636 time to fit residues: 56.9885 Evaluate side-chains 194 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 69 ILE Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AB residue 38 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CA residue 430 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 296 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068755 restraints weight = 259276.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074118 restraints weight = 82989.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074450 restraints weight = 42829.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074953 restraints weight = 38700.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077553 restraints weight = 33325.007| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31008 Z= 0.170 Angle : 0.549 9.827 42352 Z= 0.282 Chirality : 0.043 0.190 4944 Planarity : 0.003 0.045 5336 Dihedral : 6.493 51.567 6000 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.56 % Allowed : 8.87 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.07 (0.14), residues: 3680 helix: 1.50 (0.21), residues: 696 sheet: 0.51 (0.15), residues: 1088 loop : -0.99 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGGA 82 TYR 0.013 0.001 TYRAA 276 PHE 0.011 0.001 PHECA 157 TRP 0.012 0.001 TRPEA 37 HIS 0.004 0.001 HISDA 217 Details of bonding type rmsd covalent geometry : bond 0.00394 (30936) covalent geometry : angle 0.53880 (42160) SS BOND : bond 0.00175 ( 24) SS BOND : angle 0.94682 ( 48) hydrogen bonds : bond 0.04004 ( 1072) hydrogen bonds : angle 5.00657 ( 2880) link_BETA1-4 : bond 0.00358 ( 24) link_BETA1-4 : angle 2.25360 ( 72) link_NAG-ASN : bond 0.00166 ( 24) link_NAG-ASN : angle 1.28556 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.883 Fit side-chains REVERT: AA 80 MET cc_start: 0.9061 (mmt) cc_final: 0.8860 (mmt) REVERT: AB 56 SER cc_start: 0.8912 (t) cc_final: 0.8373 (p) REVERT: BA 353 MET cc_start: 0.8289 (tpt) cc_final: 0.7779 (tpt) REVERT: CA 149 MET cc_start: 0.7923 (tmm) cc_final: 0.7672 (tmm) REVERT: DA 80 MET cc_start: 0.8606 (mmm) cc_final: 0.8390 (mmm) REVERT: DA 403 MET cc_start: 0.8420 (mtm) cc_final: 0.8179 (mtm) REVERT: DB 56 SER cc_start: 0.8956 (t) cc_final: 0.8357 (p) REVERT: EA 149 MET cc_start: 0.7722 (tmm) cc_final: 0.7330 (tmm) REVERT: FB 56 SER cc_start: 0.8992 (t) cc_final: 0.8401 (p) REVERT: GA 403 MET cc_start: 0.8465 (mtm) cc_final: 0.8227 (mtm) REVERT: GB 56 SER cc_start: 0.8982 (t) cc_final: 0.8380 (p) REVERT: HA 353 MET cc_start: 0.8360 (tpt) cc_final: 0.7786 (tpt) outliers start: 52 outliers final: 45 residues processed: 207 average time/residue: 0.1466 time to fit residues: 52.7440 Evaluate side-chains 201 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 SER Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AA residue 154 LEU Chi-restraints excluded: chain AA residue 256 MET Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 254 SER Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CA residue 430 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 254 SER Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain GB residue 76 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HA residue 430 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 234 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 318 optimal weight: 8.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068268 restraints weight = 254937.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072487 restraints weight = 75173.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075347 restraints weight = 40707.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.077175 restraints weight = 28292.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078349 restraints weight = 22565.201| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31008 Z= 0.094 Angle : 0.508 12.874 42352 Z= 0.259 Chirality : 0.041 0.187 4944 Planarity : 0.003 0.039 5336 Dihedral : 6.080 54.023 6000 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.29 % Allowed : 9.14 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: 0.12 (0.14), residues: 3680 helix: 1.68 (0.22), residues: 696 sheet: 0.65 (0.15), residues: 1112 loop : -0.91 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBA 284 TYR 0.014 0.001 TYRGA 276 PHE 0.008 0.001 PHECA 157 TRP 0.013 0.001 TRPBA 37 HIS 0.003 0.001 HISFA 431 Details of bonding type rmsd covalent geometry : bond 0.00206 (30936) covalent geometry : angle 0.50047 (42160) SS BOND : bond 0.00346 ( 24) SS BOND : angle 0.80104 ( 48) hydrogen bonds : bond 0.03223 ( 1072) hydrogen bonds : angle 4.79473 ( 2880) link_BETA1-4 : bond 0.00400 ( 24) link_BETA1-4 : angle 1.90327 ( 72) link_NAG-ASN : bond 0.00333 ( 24) link_NAG-ASN : angle 1.12343 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 1.019 Fit side-chains REVERT: AA 80 MET cc_start: 0.9073 (mmt) cc_final: 0.8856 (mmt) REVERT: AB 56 SER cc_start: 0.8915 (t) cc_final: 0.8295 (p) REVERT: BA 353 MET cc_start: 0.8276 (tpt) cc_final: 0.7773 (tpt) REVERT: CA 80 MET cc_start: 0.7252 (mmm) cc_final: 0.6886 (mmm) REVERT: CA 149 MET cc_start: 0.7881 (tmm) cc_final: 0.7628 (tmm) REVERT: CB 75 ASN cc_start: 0.8683 (p0) cc_final: 0.8433 (p0) REVERT: DA 80 MET cc_start: 0.8624 (mmm) cc_final: 0.8387 (mmm) REVERT: DA 403 MET cc_start: 0.8480 (mtm) cc_final: 0.8260 (mtm) REVERT: DB 56 SER cc_start: 0.8873 (t) cc_final: 0.8256 (p) REVERT: EA 80 MET cc_start: 0.7299 (mmm) cc_final: 0.6907 (mmm) REVERT: EA 149 MET cc_start: 0.7647 (tmm) cc_final: 0.7220 (tmm) REVERT: FB 56 SER cc_start: 0.8892 (t) cc_final: 0.8287 (p) REVERT: GA 403 MET cc_start: 0.8493 (mtm) cc_final: 0.8249 (mtm) REVERT: GB 56 SER cc_start: 0.8880 (t) cc_final: 0.8267 (p) REVERT: HA 353 MET cc_start: 0.8277 (tpt) cc_final: 0.7773 (tpt) outliers start: 43 outliers final: 34 residues processed: 206 average time/residue: 0.1517 time to fit residues: 55.0180 Evaluate side-chains 197 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 254 SER Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 254 SER Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 105 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067415 restraints weight = 268935.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072003 restraints weight = 91426.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072064 restraints weight = 54008.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073212 restraints weight = 41561.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073851 restraints weight = 37248.175| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 31008 Z= 0.321 Angle : 0.685 14.939 42352 Z= 0.345 Chirality : 0.047 0.216 4944 Planarity : 0.004 0.058 5336 Dihedral : 6.908 54.717 6000 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.53 % Allowed : 9.05 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -0.25 (0.14), residues: 3680 helix: 1.15 (0.21), residues: 696 sheet: 0.39 (0.15), residues: 1128 loop : -1.04 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAA 134 TYR 0.021 0.002 TYRAA 277 PHE 0.019 0.002 PHEHA 157 TRP 0.012 0.002 TRPCA 37 HIS 0.006 0.002 HISGA 217 Details of bonding type rmsd covalent geometry : bond 0.00749 (30936) covalent geometry : angle 0.67276 (42160) SS BOND : bond 0.00275 ( 24) SS BOND : angle 1.64336 ( 48) hydrogen bonds : bond 0.05093 ( 1072) hydrogen bonds : angle 5.33193 ( 2880) link_BETA1-4 : bond 0.00306 ( 24) link_BETA1-4 : angle 2.61023 ( 72) link_NAG-ASN : bond 0.00461 ( 24) link_NAG-ASN : angle 1.61460 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.257 Fit side-chains REVERT: AA 80 MET cc_start: 0.9009 (mmt) cc_final: 0.8764 (mmt) REVERT: AB 56 SER cc_start: 0.8954 (t) cc_final: 0.8403 (p) REVERT: BA 353 MET cc_start: 0.8295 (tpt) cc_final: 0.7799 (tpt) REVERT: CA 149 MET cc_start: 0.7978 (tmm) cc_final: 0.7773 (tmm) REVERT: DA 403 MET cc_start: 0.8394 (mtm) cc_final: 0.8170 (mtm) REVERT: DB 56 SER cc_start: 0.8913 (t) cc_final: 0.8379 (p) REVERT: FB 56 SER cc_start: 0.8931 (t) cc_final: 0.8398 (p) REVERT: GA 403 MET cc_start: 0.8383 (mtm) cc_final: 0.8152 (mtm) REVERT: GB 56 SER cc_start: 0.8961 (t) cc_final: 0.8405 (p) REVERT: HA 353 MET cc_start: 0.8324 (tpt) cc_final: 0.7823 (tpt) outliers start: 51 outliers final: 46 residues processed: 209 average time/residue: 0.1634 time to fit residues: 59.7283 Evaluate side-chains 211 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AB residue 38 VAL Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 254 SER Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CA residue 430 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 253 ILE Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FA residue 89 SER Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain FB residue 76 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 125 SER Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GA residue 202 MET Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HA residue 430 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 14 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.069106 restraints weight = 303753.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075051 restraints weight = 89400.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075057 restraints weight = 42566.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075656 restraints weight = 39190.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078747 restraints weight = 32959.759| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31008 Z= 0.135 Angle : 0.556 13.637 42352 Z= 0.282 Chirality : 0.042 0.209 4944 Planarity : 0.003 0.061 5336 Dihedral : 6.384 53.340 6000 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 1.44 % Allowed : 9.11 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.02 (0.14), residues: 3680 helix: 1.52 (0.21), residues: 696 sheet: 0.51 (0.15), residues: 1112 loop : -0.94 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAA 134 TYR 0.011 0.001 TYRCA 377 PHE 0.010 0.001 PHEEA 157 TRP 0.015 0.001 TRPBA 37 HIS 0.003 0.001 HISFA 431 Details of bonding type rmsd covalent geometry : bond 0.00310 (30936) covalent geometry : angle 0.54305 (42160) SS BOND : bond 0.00145 ( 24) SS BOND : angle 2.23570 ( 48) hydrogen bonds : bond 0.03661 ( 1072) hydrogen bonds : angle 5.00435 ( 2880) link_BETA1-4 : bond 0.00416 ( 24) link_BETA1-4 : angle 2.05748 ( 72) link_NAG-ASN : bond 0.00251 ( 24) link_NAG-ASN : angle 1.31038 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.244 Fit side-chains REVERT: AB 56 SER cc_start: 0.8958 (t) cc_final: 0.8367 (p) REVERT: BA 353 MET cc_start: 0.8277 (tpt) cc_final: 0.7762 (tpt) REVERT: CA 149 MET cc_start: 0.7917 (tmm) cc_final: 0.7711 (tmm) REVERT: DA 403 MET cc_start: 0.8458 (mtm) cc_final: 0.8226 (mtm) REVERT: DB 56 SER cc_start: 0.8934 (t) cc_final: 0.8355 (p) REVERT: FB 56 SER cc_start: 0.8972 (t) cc_final: 0.8385 (p) REVERT: GA 403 MET cc_start: 0.8402 (mtm) cc_final: 0.8182 (mtm) REVERT: GB 56 SER cc_start: 0.8966 (t) cc_final: 0.8372 (p) REVERT: HA 353 MET cc_start: 0.8248 (tpt) cc_final: 0.7757 (tpt) outliers start: 48 outliers final: 43 residues processed: 202 average time/residue: 0.1567 time to fit residues: 55.2548 Evaluate side-chains 203 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain AB residue 73 ASP Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 254 SER Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 254 SER Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 254 SER Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 345 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 308 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 295 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069591 restraints weight = 258188.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.074217 restraints weight = 89879.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074383 restraints weight = 52113.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075537 restraints weight = 40739.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076699 restraints weight = 35652.196| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31008 Z= 0.158 Angle : 0.568 13.585 42352 Z= 0.288 Chirality : 0.043 0.252 4944 Planarity : 0.003 0.038 5336 Dihedral : 6.353 52.791 6000 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 1.32 % Allowed : 9.35 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -0.06 (0.14), residues: 3680 helix: 1.49 (0.21), residues: 696 sheet: 0.39 (0.15), residues: 1128 loop : -0.90 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGFA 134 TYR 0.011 0.001 TYRCA 377 PHE 0.011 0.001 PHEAA 157 TRP 0.013 0.001 TRPCA 37 HIS 0.004 0.001 HISGA 224 Details of bonding type rmsd covalent geometry : bond 0.00365 (30936) covalent geometry : angle 0.55403 (42160) SS BOND : bond 0.00245 ( 24) SS BOND : angle 2.46272 ( 48) hydrogen bonds : bond 0.03821 ( 1072) hydrogen bonds : angle 4.97068 ( 2880) link_BETA1-4 : bond 0.00350 ( 24) link_BETA1-4 : angle 2.09991 ( 72) link_NAG-ASN : bond 0.00130 ( 24) link_NAG-ASN : angle 1.34802 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7360 Ramachandran restraints generated. 3680 Oldfield, 0 Emsley, 3680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.905 Fit side-chains REVERT: AA 80 MET cc_start: 0.8920 (mmt) cc_final: 0.8703 (mmt) REVERT: AB 56 SER cc_start: 0.8976 (t) cc_final: 0.8372 (p) REVERT: BA 353 MET cc_start: 0.8304 (tpt) cc_final: 0.7795 (tpt) REVERT: CA 149 MET cc_start: 0.7938 (tmm) cc_final: 0.7732 (tmm) REVERT: DA 403 MET cc_start: 0.8375 (mtm) cc_final: 0.8147 (mtm) REVERT: DB 56 SER cc_start: 0.8954 (t) cc_final: 0.8362 (p) REVERT: FB 56 SER cc_start: 0.9004 (t) cc_final: 0.8405 (p) REVERT: GA 403 MET cc_start: 0.8383 (mtm) cc_final: 0.8149 (mtm) REVERT: GB 56 SER cc_start: 0.9002 (t) cc_final: 0.8405 (p) REVERT: HA 353 MET cc_start: 0.8282 (tpt) cc_final: 0.7782 (tpt) outliers start: 44 outliers final: 42 residues processed: 199 average time/residue: 0.1419 time to fit residues: 49.2705 Evaluate side-chains 197 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 125 SER Chi-restraints excluded: chain AA residue 150 CYS Chi-restraints excluded: chain AB residue 58 VAL Chi-restraints excluded: chain BA residue 90 LEU Chi-restraints excluded: chain BA residue 97 VAL Chi-restraints excluded: chain BA residue 154 LEU Chi-restraints excluded: chain BA residue 195 CYS Chi-restraints excluded: chain BA residue 254 SER Chi-restraints excluded: chain BA residue 378 ILE Chi-restraints excluded: chain CA residue 90 LEU Chi-restraints excluded: chain CA residue 97 VAL Chi-restraints excluded: chain CA residue 195 CYS Chi-restraints excluded: chain CA residue 242 ILE Chi-restraints excluded: chain CA residue 254 SER Chi-restraints excluded: chain CA residue 256 MET Chi-restraints excluded: chain CA residue 351 LEU Chi-restraints excluded: chain CA residue 378 ILE Chi-restraints excluded: chain CB residue 71 LEU Chi-restraints excluded: chain DA residue 90 LEU Chi-restraints excluded: chain DA residue 150 CYS Chi-restraints excluded: chain DB residue 58 VAL Chi-restraints excluded: chain EA residue 90 LEU Chi-restraints excluded: chain EA residue 97 VAL Chi-restraints excluded: chain EA residue 125 SER Chi-restraints excluded: chain EA residue 195 CYS Chi-restraints excluded: chain EA residue 254 SER Chi-restraints excluded: chain EA residue 256 MET Chi-restraints excluded: chain EA residue 378 ILE Chi-restraints excluded: chain EA residue 430 ILE Chi-restraints excluded: chain FA residue 150 CYS Chi-restraints excluded: chain FB residue 58 VAL Chi-restraints excluded: chain GA residue 89 SER Chi-restraints excluded: chain GA residue 90 LEU Chi-restraints excluded: chain GA residue 150 CYS Chi-restraints excluded: chain GB residue 58 VAL Chi-restraints excluded: chain HA residue 90 LEU Chi-restraints excluded: chain HA residue 97 VAL Chi-restraints excluded: chain HA residue 125 SER Chi-restraints excluded: chain HA residue 195 CYS Chi-restraints excluded: chain HA residue 256 MET Chi-restraints excluded: chain HA residue 378 ILE Chi-restraints excluded: chain HB residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 286 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 233 optimal weight: 0.2980 chunk 248 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 349 optimal weight: 0.0010 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070171 restraints weight = 290391.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075911 restraints weight = 87070.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076103 restraints weight = 42293.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.076697 restraints weight = 38183.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079744 restraints weight = 32451.362| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31008 Z= 0.101 Angle : 0.531 13.090 42352 Z= 0.270 Chirality : 0.042 0.250 4944 Planarity : 0.003 0.036 5336 Dihedral : 6.063 53.924 6000 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.17 % Allowed : 9.47 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3680 helix: 1.64 (0.22), residues: 696 sheet: 0.51 (0.16), residues: 1072 loop : -0.86 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGEA 284 TYR 0.012 0.001 TYRCA 377 PHE 0.008 0.001 PHEFA 426 TRP 0.014 0.001 TRPCA 37 HIS 0.003 0.001 HISAA 431 Details of bonding type rmsd covalent geometry : bond 0.00223 (30936) covalent geometry : angle 0.51911 (42160) SS BOND : bond 0.00131 ( 24) SS BOND : angle 2.19700 ( 48) hydrogen bonds : bond 0.03261 ( 1072) hydrogen bonds : angle 4.81374 ( 2880) link_BETA1-4 : bond 0.00415 ( 24) link_BETA1-4 : angle 1.89030 ( 72) link_NAG-ASN : bond 0.00253 ( 24) link_NAG-ASN : angle 1.19832 ( 72) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4132.90 seconds wall clock time: 71 minutes 50.52 seconds (4310.52 seconds total)