Starting phenix.real_space_refine on Fri Nov 21 02:09:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6did_7896/11_2025/6did_7896.cif Found real_map, /net/cci-nas-00/data/ceres_data/6did_7896/11_2025/6did_7896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6did_7896/11_2025/6did_7896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6did_7896/11_2025/6did_7896.map" model { file = "/net/cci-nas-00/data/ceres_data/6did_7896/11_2025/6did_7896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6did_7896/11_2025/6did_7896.cif" } resolution = 4.71 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= 0.004 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9762 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 162 5.16 5 C 15699 2.51 5 N 4089 2.21 5 O 5259 1.98 5 H 9465 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34674 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 3258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3068 Chain: "D" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} bond proxies already assigned to first conformer: 3024 Chain: "E" Number of atoms: 3258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3068 Chain: "K" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} bond proxies already assigned to first conformer: 3024 Chain: "H" Number of atoms: 3258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 217, 3149 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3068 Chain: "L" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 213, 3071 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} bond proxies already assigned to first conformer: 3024 Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "p" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 90 residue: pdb=" N ACYS C 43 " occ=0.68 ... (18 atoms not shown) pdb=" HB3BCYS C 43 " occ=0.32 residue: pdb=" N ALYS C 65 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS C 65 " occ=0.50 residue: pdb=" N ALYS C 133 " occ=0.47 ... (42 atoms not shown) pdb=" HZ3BLYS C 133 " occ=0.53 residue: pdb=" N AVAL C 137 " occ=0.81 ... (30 atoms not shown) pdb="HG23BVAL C 137 " occ=0.19 residue: pdb=" N ASER C 140 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER C 140 " occ=0.50 residue: pdb=" N ATHR C 170 " occ=0.38 ... (26 atoms not shown) pdb="HG23BTHR C 170 " occ=0.62 residue: pdb=" N ATHR C 172 " occ=0.25 ... (26 atoms not shown) pdb="HG23BTHR C 172 " occ=0.75 residue: pdb=" N APHE D 87 " occ=0.56 ... (38 atoms not shown) pdb=" HZ BPHE D 87 " occ=0.44 residue: pdb=" N ACYS D 114 " occ=0.75 ... (18 atoms not shown) pdb=" HB3BCYS D 114 " occ=0.25 residue: pdb=" N ATHR D 174 " occ=0.49 ... (26 atoms not shown) pdb="HG23BTHR D 174 " occ=0.51 residue: pdb=" N AARG D 193 " occ=0.54 ... (46 atoms not shown) pdb="HH22BARG D 193 " occ=0.46 residue: pdb=" N ASER D 211 " occ=0.51 ... (20 atoms not shown) pdb=" HG BSER D 211 " occ=0.49 ... (remaining 78 not shown) Time building chain proxies: 9.93, per 1000 atoms: 0.29 Number of scatterers: 34674 At special positions: 0 Unit cell: (186.3, 195.5, 134.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 O 5259 8.00 N 4089 7.00 C 15699 6.00 H 9465 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.19 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.19 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.11 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.19 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.11 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG ACYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG BCYS C 43 " distance=2.01 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 219 " distance=2.03 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS D 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG ACYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG BCYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 69 " distance=2.07 Simple disulfide: pdb=" SG CYS D 163 " - pdb=" SG CYS D 216 " distance=2.04 Simple disulfide: pdb=" SG ACYS E 43 " - pdb=" SG CYS E 108 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG BCYS E 43 " distance=2.01 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS K 150 " distance=2.02 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG ACYS K 114 " distance=2.03 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG BCYS K 114 " distance=2.02 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 69 " distance=2.07 Simple disulfide: pdb=" SG CYS K 163 " - pdb=" SG CYS K 216 " distance=2.04 Simple disulfide: pdb=" SG ACYS H 43 " - pdb=" SG CYS H 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG BCYS H 43 " distance=2.01 Simple disulfide: pdb=" SG CYS H 160 " - pdb=" SG CYS H 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS L 150 " distance=2.02 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG ACYS L 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG BCYS L 114 " distance=2.02 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 69 " distance=2.06 Simple disulfide: pdb=" SG CYS L 163 " - pdb=" SG CYS L 216 " distance=2.04 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=3, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN c 4 " - " MAN c 5 " " MAN d 4 " - " MAN d 5 " " MAN o 4 " - " MAN o 5 " " MAN p 4 " - " MAN p 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " " BMA o 3 " - " MAN o 4 " " MAN o 6 " - " MAN o 7 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA t 3 " - " MAN t 6 " " MAN t 4 " - " MAN t 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 6 " " MAN d 6 " - " MAN d 8 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 6 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA t 3 " - " MAN t 4 " " BMA u 3 " - " MAN u 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 604 " - " ASN A 133 " " NAG A 611 " - " ASN A 234 " " NAG A 633 " - " ASN A 339 " " NAG A 634 " - " ASN A 355 " " NAG A 645 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG F 604 " - " ASN F 133 " " NAG F 611 " - " ASN F 234 " " NAG F 631 " - " ASN F 355 " " NAG F 634 " - " ASN F 339 " " NAG F 645 " - " ASN F 392 " " NAG G 604 " - " ASN G 133 " " NAG G 611 " - " ASN G 234 " " NAG G 633 " - " ASN G 339 " " NAG G 634 " - " ASN G 355 " " NAG G 645 " - " ASN G 392 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 637 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN F 88 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 160 " " NAG b 1 " - " ASN F 197 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN F 276 " " NAG e 1 " - " ASN F 295 " " NAG f 1 " - " ASN F 301 " " NAG g 1 " - " ASN F 332 " " NAG h 1 " - " ASN F 363 " " NAG i 1 " - " ASN F 386 " " NAG j 1 " - " ASN F 448 " " NAG k 1 " - " ASN G 88 " " NAG l 1 " - " ASN G 156 " " NAG m 1 " - " ASN G 160 " " NAG n 1 " - " ASN G 197 " " NAG o 1 " - " ASN G 262 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 301 " " NAG s 1 " - " ASN G 332 " " NAG t 1 " - " ASN G 363 " " NAG u 1 " - " ASN G 386 " " NAG v 1 " - " ASN G 448 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 60 sheets defined 20.3% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.823A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.966A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.744A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'F' and resid 99 through 117 removed outlier: 3.825A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.864A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 377 through 381 removed outlier: 3.501A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.968A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 Processing helix chain 'I' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER I 534 " --> pdb=" O MET I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG I 542 " --> pdb=" O THR I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 597 Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 649 Processing helix chain 'I' and resid 650 through 663 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.824A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.865A pdb=" N VAL G 127 " --> pdb=" O PRO G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.500A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.966A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 Processing helix chain 'J' and resid 529 through 534 removed outlier: 3.745A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.581A pdb=" N ARG J 542 " --> pdb=" O THR J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 Processing helix chain 'J' and resid 650 through 663 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 147 through 153 removed outlier: 4.063A pdb=" N VAL C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 153' Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.529A pdb=" N HIS C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'D' and resid 105 through 109 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 221 through 224 Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 147 through 153 removed outlier: 4.063A pdb=" N VAL E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 147 through 153' Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.529A pdb=" N HIS E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 179 through 181 No H-bonds generated for 'chain 'K' and resid 179 through 181' Processing helix chain 'K' and resid 221 through 224 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 147 through 153 removed outlier: 4.063A pdb=" N VAL H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA H 152 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR H 153 " --> pdb=" O ASP H 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 147 through 153' Processing helix chain 'H' and resid 208 through 214 removed outlier: 3.529A pdb=" N HIS H 214 " --> pdb=" O GLN H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 221 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.057A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.410A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AB6, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AB9, first strand: chain 'F' and resid 394 through 395 removed outlier: 6.668A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.055A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 316 through 323 removed outlier: 4.411A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.863A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AC7, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AC8, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 202 Processing sheet with id=AD1, first strand: chain 'G' and resid 394 through 395 removed outlier: 6.669A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.056A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 316 through 323 removed outlier: 4.410A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.831A pdb=" N GLN C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 30 through 34 removed outlier: 6.336A pdb=" N VAL C 31 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALYS C 133 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA C 33 " --> pdb=" O ALYS C 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 69 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.101A pdb=" N TYR C 198 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 178 through 179 Processing sheet with id=AD8, first strand: chain 'D' and resid 23 through 25 removed outlier: 6.176A pdb=" N THR D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY D 28 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET D 53 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY D 28 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 125 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR D 199 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR D 199 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 174 through 177 Processing sheet with id=AE5, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.831A pdb=" N GLN E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 30 through 34 removed outlier: 6.337A pdb=" N VAL E 31 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALYS E 133 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA E 33 " --> pdb=" O ALYS E 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 53 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR E 69 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.101A pdb=" N TYR E 198 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AE9, first strand: chain 'K' and resid 23 through 25 removed outlier: 6.176A pdb=" N THR K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 28 through 30 removed outlier: 6.090A pdb=" N GLY K 28 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET K 53 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS K 69 " --> pdb=" O MET K 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP K 55 " --> pdb=" O ILE K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 28 through 30 removed outlier: 6.090A pdb=" N GLY K 28 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU K 125 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR K 199 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR K 199 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 174 through 177 Processing sheet with id=AF6, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.832A pdb=" N GLN H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 30 through 34 removed outlier: 6.337A pdb=" N VAL H 31 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALYS H 133 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA H 33 " --> pdb=" O ALYS H 133 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR H 69 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 140 through 144 removed outlier: 6.101A pdb=" N TYR H 198 " --> pdb=" O LYS H 164 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 178 through 179 Processing sheet with id=AG1, first strand: chain 'L' and resid 23 through 25 removed outlier: 6.176A pdb=" N THR L 96 " --> pdb=" O THR L 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY L 28 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET L 53 " --> pdb=" O CYS L 69 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS L 69 " --> pdb=" O MET L 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP L 55 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 28 through 30 removed outlier: 6.089A pdb=" N GLY L 28 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU L 125 " --> pdb=" O ARG L 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR L 199 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 143 through 147 removed outlier: 5.559A pdb=" N TYR L 199 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 174 through 177 1023 hydrogen bonds defined for protein. 2556 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: 11.31 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9462 1.04 - 1.25: 3839 1.25 - 1.46: 9907 1.46 - 1.66: 11787 1.66 - 1.87: 207 Bond restraints: 35202 Sorted by residual: bond pdb=" C3 MAN d 5 " pdb=" C4 MAN d 5 " ideal model delta sigma weight residual 1.524 1.615 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C3 MAN p 5 " pdb=" C4 MAN p 5 " ideal model delta sigma weight residual 1.524 1.614 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 MAN R 5 " pdb=" C4 MAN R 5 " ideal model delta sigma weight residual 1.524 1.614 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CA ILE B 641 " pdb=" C ILE B 641 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" C4 MAN R 5 " pdb=" C5 MAN R 5 " ideal model delta sigma weight residual 1.533 1.619 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 35197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 53116 2.53 - 5.06: 2801 5.06 - 7.59: 513 7.59 - 10.12: 84 10.12 - 12.65: 18 Bond angle restraints: 56532 Sorted by residual: angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 120.12 131.59 -11.47 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 120.12 131.54 -11.42 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C LYS F 252 " pdb=" N PRO F 253 " pdb=" CA PRO F 253 " ideal model delta sigma weight residual 120.12 131.53 -11.41 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C CYS F 239 " pdb=" N PRO F 240 " pdb=" CA PRO F 240 " ideal model delta sigma weight residual 119.56 129.04 -9.48 1.01e+00 9.80e-01 8.80e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 129.02 -9.46 1.01e+00 9.80e-01 8.77e+01 ... (remaining 56527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 19716 22.84 - 45.69: 743 45.69 - 68.53: 265 68.53 - 91.38: 106 91.38 - 114.22: 44 Dihedral angle restraints: 20874 sinusoidal: 11490 harmonic: 9384 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.26 44.26 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.24 44.24 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.18 44.18 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 20871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4170 0.175 - 0.350: 258 0.350 - 0.526: 48 0.526 - 0.701: 3 0.701 - 0.876: 3 Chirality restraints: 4482 Sorted by residual: chirality pdb=" C1 MAN R 6 " pdb=" O6 BMA R 3 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.92e+03 chirality pdb=" C1 MAN d 6 " pdb=" O6 BMA d 3 " pdb=" C2 MAN d 6 " pdb=" O5 MAN d 6 " both_signs ideal model delta sigma weight residual False 2.40 1.52 0.88 2.00e-02 2.50e+03 1.91e+03 chirality pdb=" C1 MAN p 6 " pdb=" O6 BMA p 3 " pdb=" C2 MAN p 6 " pdb=" O5 MAN p 6 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.91e+03 ... (remaining 4479 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 363 " 0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN G 363 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN G 363 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN G 363 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG t 1 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 363 " 0.195 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" CG ASN A 363 " -0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 363 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 363 " -0.443 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 363 " -0.195 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" CG ASN F 363 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN F 363 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 363 " 0.443 2.00e-02 2.50e+03 pdb=" C1 NAG h 1 " -0.319 2.00e-02 2.50e+03 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 0.72 - 1.49: 25 1.49 - 2.27: 3208 2.27 - 3.05: 68485 3.05 - 3.82: 115467 3.82 - 4.60: 187629 Warning: very small nonbonded interaction distances. Nonbonded interactions: 374814 Sorted by model distance: nonbonded pdb=" NZ LYS A 231 " pdb=" OH TYR L 52 " model vdw 0.718 2.950 nonbonded pdb=" NZ LYS F 231 " pdb=" OH TYR D 52 " model vdw 0.726 2.950 nonbonded pdb=" NZ LYS G 231 " pdb=" OH TYR K 52 " model vdw 0.726 2.950 nonbonded pdb=" N PRO F 240 " pdb="HH21 ARG C 50 " model vdw 0.973 2.080 nonbonded pdb=" N PRO A 240 " pdb="HH21 ARG H 50 " model vdw 0.998 2.080 ... (remaining 374809 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'C' and (resid 21 through 42 or resid 44 through 64 or resid 66 through 1 \ 32 or resid 134 through 136 or resid 138 through 139 or resid 141 through 169 or \ resid 171 or resid 173 through 237)) selection = (chain 'E' and (resid 21 through 42 or resid 44 through 64 or resid 66 through 1 \ 32 or resid 134 through 136 or resid 138 through 139 or resid 141 through 169 or \ resid 171 or resid 173 through 237)) selection = (chain 'H' and (resid 21 through 42 or resid 44 through 64 or resid 66 through 1 \ 32 or resid 134 through 136 or resid 138 through 139 or resid 141 through 169 or \ resid 171 or resid 173 through 237)) } ncs_group { reference = (chain 'D' and (resid 22 through 86 or resid 88 through 113 or resid 115 through \ 173 or resid 175 through 192 or resid 194 through 210 or resid 213 through 234) \ ) selection = (chain 'K' and (resid 22 through 86 or resid 88 through 113 or resid 115 through \ 173 or resid 175 through 192 or resid 194 through 210 or resid 213 through 234) \ ) selection = (chain 'L' and (resid 22 through 86 or resid 88 through 113 or resid 115 through \ 173 or resid 175 through 192 or resid 194 through 210 or resid 213 through 234) \ ) } ncs_group { reference = chain 'M' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'v' } ncs_group { reference = (chain 'Q' and resid 5 through 7) selection = (chain 'R' and resid 6 through 8) selection = (chain 'V' and resid 4 through 6) selection = (chain 'c' and resid 5 through 7) selection = (chain 'd' and resid 6 through 8) selection = (chain 'h' and resid 4 through 6) selection = (chain 'o' and resid 5 through 7) selection = (chain 'p' and resid 6 through 8) selection = (chain 't' and resid 4 through 6) } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'u' } 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=0.00 max=1.00 mean=0.97 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.310 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 40.820 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 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 : 0.016 0.635 25947 Z= 1.059 Angle : 1.830 25.690 35679 Z= 1.007 Chirality : 0.102 0.876 4482 Planarity : 0.010 0.087 4272 Dihedral : 15.537 114.220 11523 Min Nonbonded Distance : 0.718 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.83 % Allowed : 2.17 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.15), residues: 3066 helix: -0.71 (0.22), residues: 414 sheet: 0.76 (0.15), residues: 1149 loop : 1.69 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 57 TYR 0.036 0.005 TYR G 318 PHE 0.023 0.005 PHE H 91 TRP 0.052 0.007 TRP F 479 HIS 0.010 0.003 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01404 (25737) covalent geometry : angle 1.60682 (35118) SS BOND : bond 0.04124 ( 60) SS BOND : angle 2.62167 ( 120) hydrogen bonds : bond 0.15859 ( 963) hydrogen bonds : angle 8.16273 ( 2556) Misc. bond : bond 0.60943 ( 3) link_ALPHA1-2 : bond 0.02124 ( 6) link_ALPHA1-2 : angle 3.75098 ( 18) link_ALPHA1-3 : bond 0.03206 ( 18) link_ALPHA1-3 : angle 3.20075 ( 54) link_ALPHA1-6 : bond 0.02864 ( 15) link_ALPHA1-6 : angle 6.75122 ( 45) link_BETA1-4 : bond 0.02973 ( 51) link_BETA1-4 : angle 4.98248 ( 153) link_NAG-ASN : bond 0.02753 ( 57) link_NAG-ASN : angle 11.17192 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8409 (ttt) cc_final: 0.8175 (ttm) REVERT: A 114 GLN cc_start: 0.9097 (tp40) cc_final: 0.8825 (tm-30) REVERT: A 475 MET cc_start: 0.8893 (mmp) cc_final: 0.8570 (mmm) REVERT: B 530 MET cc_start: 0.8943 (mtp) cc_final: 0.8738 (mtt) REVERT: B 536 THR cc_start: 0.9098 (p) cc_final: 0.8752 (t) REVERT: B 595 ILE cc_start: 0.9700 (mt) cc_final: 0.9486 (mm) REVERT: F 475 MET cc_start: 0.8936 (mmp) cc_final: 0.8465 (mmm) REVERT: I 530 MET cc_start: 0.9011 (mtp) cc_final: 0.8795 (mtt) REVERT: I 536 THR cc_start: 0.9097 (p) cc_final: 0.8761 (t) REVERT: I 595 ILE cc_start: 0.9735 (mt) cc_final: 0.9529 (mm) REVERT: G 475 MET cc_start: 0.8822 (mmp) cc_final: 0.8424 (mmm) REVERT: J 536 THR cc_start: 0.9067 (p) cc_final: 0.8700 (t) REVERT: C 89 THR cc_start: 0.6413 (OUTLIER) cc_final: 0.5953 (t) REVERT: D 70 ILE cc_start: 0.8679 (tt) cc_final: 0.8418 (tt) REVERT: E 89 THR cc_start: 0.6006 (OUTLIER) cc_final: 0.5534 (t) REVERT: E 149 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: K 97 VAL cc_start: 0.7039 (t) cc_final: 0.6825 (t) REVERT: H 89 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5688 (t) REVERT: H 149 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: H 233 ASN cc_start: 0.5305 (m-40) cc_final: 0.4550 (m110) REVERT: L 70 ILE cc_start: 0.8733 (tt) cc_final: 0.8469 (tt) outliers start: 45 outliers final: 8 residues processed: 376 average time/residue: 0.3056 time to fit residues: 172.8442 Evaluate side-chains 228 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN D 194 GLN E 214 HIS L 194 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.090699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.071787 restraints weight = 1735359.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.073952 restraints weight = 426905.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.075165 restraints weight = 193933.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.075730 restraints weight = 127247.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.076069 restraints weight = 105459.657| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 630 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1004 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 25947 Z= 0.227 Angle : 0.913 18.087 35679 Z= 0.432 Chirality : 0.048 0.303 4482 Planarity : 0.007 0.228 4272 Dihedral : 13.939 77.004 6252 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.16 % Favored : 97.74 % Rotamer: Outliers : 0.30 % Allowed : 1.07 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 are not related in a simple way. whole: 1.34 (0.15), residues: 3066 helix: 1.01 (0.26), residues: 414 sheet: 0.51 (0.14), residues: 1215 loop : 1.48 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 50 TYR 0.025 0.002 TYR E 52 PHE 0.020 0.002 PHE F 353 TRP 0.025 0.002 TRP F 69 HIS 0.011 0.002 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00456 (25737) covalent geometry : angle 0.80349 (35118) SS BOND : bond 0.00468 ( 60) SS BOND : angle 2.12685 ( 120) hydrogen bonds : bond 0.04901 ( 963) hydrogen bonds : angle 6.63384 ( 2556) Misc. bond : bond 0.01796 ( 3) link_ALPHA1-2 : bond 0.00144 ( 6) link_ALPHA1-2 : angle 2.00255 ( 18) link_ALPHA1-3 : bond 0.00398 ( 18) link_ALPHA1-3 : angle 2.21362 ( 54) link_ALPHA1-6 : bond 0.00756 ( 15) link_ALPHA1-6 : angle 2.22741 ( 45) link_BETA1-4 : bond 0.00509 ( 51) link_BETA1-4 : angle 2.74031 ( 153) link_NAG-ASN : bond 0.00932 ( 57) link_NAG-ASN : angle 5.30746 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 244 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9395 (tmm) cc_final: 0.9114 (ppp) REVERT: A 107 ASP cc_start: 0.9486 (t70) cc_final: 0.8999 (t0) REVERT: A 114 GLN cc_start: 0.9637 (tp40) cc_final: 0.9242 (tm-30) REVERT: B 647 GLU cc_start: 0.8809 (tt0) cc_final: 0.8521 (tt0) REVERT: F 69 TRP cc_start: 0.8701 (m100) cc_final: 0.8245 (m100) REVERT: F 104 MET cc_start: 0.9464 (tmm) cc_final: 0.9215 (ppp) REVERT: F 107 ASP cc_start: 0.9370 (t70) cc_final: 0.8967 (t0) REVERT: G 45 TRP cc_start: 0.8160 (m-90) cc_final: 0.7911 (m-90) REVERT: G 69 TRP cc_start: 0.8794 (m100) cc_final: 0.8386 (m100) REVERT: G 161 MET cc_start: 0.9237 (tmm) cc_final: 0.9026 (tmm) REVERT: C 108 CYS cc_start: 0.8153 (t) cc_final: 0.6340 (m) REVERT: D 76 ILE cc_start: 0.7665 (mm) cc_final: 0.7456 (mt) REVERT: E 108 CYS cc_start: 0.8162 (t) cc_final: 0.6333 (m) REVERT: H 108 CYS cc_start: 0.8389 (t) cc_final: 0.6886 (m) outliers start: 5 outliers final: 0 residues processed: 249 average time/residue: 0.3280 time to fit residues: 121.2841 Evaluate side-chains 188 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 125 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 79 optimal weight: 0.0980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN I 618 ASN G 170 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN D 194 GLN L 194 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.090233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.071200 restraints weight = 1806043.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.073348 restraints weight = 428408.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.074510 restraints weight = 193221.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.075228 restraints weight = 127518.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.075467 restraints weight = 103612.470| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1004 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1012 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25947 Z= 0.163 Angle : 0.786 23.597 35679 Z= 0.367 Chirality : 0.053 1.110 4482 Planarity : 0.005 0.140 4272 Dihedral : 11.624 71.951 6252 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.30 % Allowed : 1.45 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.15), residues: 3066 helix: 1.44 (0.27), residues: 411 sheet: 0.38 (0.14), residues: 1236 loop : 1.34 (0.18), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 50 TYR 0.023 0.002 TYR G 217 PHE 0.022 0.002 PHE D 145 TRP 0.014 0.001 TRP F 69 HIS 0.006 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00330 (25737) covalent geometry : angle 0.67239 (35118) SS BOND : bond 0.00747 ( 60) SS BOND : angle 1.84291 ( 120) hydrogen bonds : bond 0.03863 ( 963) hydrogen bonds : angle 6.03569 ( 2556) Misc. bond : bond 0.00856 ( 3) link_ALPHA1-2 : bond 0.00137 ( 6) link_ALPHA1-2 : angle 1.91261 ( 18) link_ALPHA1-3 : bond 0.00579 ( 18) link_ALPHA1-3 : angle 1.72333 ( 54) link_ALPHA1-6 : bond 0.00761 ( 15) link_ALPHA1-6 : angle 2.27265 ( 45) link_BETA1-4 : bond 0.00536 ( 51) link_BETA1-4 : angle 2.71569 ( 153) link_NAG-ASN : bond 0.00606 ( 57) link_NAG-ASN : angle 4.93595 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9390 (tmm) cc_final: 0.9127 (tmm) REVERT: A 114 GLN cc_start: 0.9634 (tp40) cc_final: 0.9285 (tm-30) REVERT: B 626 MET cc_start: 0.9109 (ptm) cc_final: 0.8852 (ttp) REVERT: F 69 TRP cc_start: 0.8638 (m100) cc_final: 0.8279 (m100) REVERT: F 100 MET cc_start: 0.9303 (ptp) cc_final: 0.8883 (ptp) REVERT: F 104 MET cc_start: 0.9457 (tmm) cc_final: 0.9228 (tmm) REVERT: G 45 TRP cc_start: 0.8062 (m-90) cc_final: 0.7825 (m-90) REVERT: G 69 TRP cc_start: 0.8697 (m100) cc_final: 0.7911 (m100) REVERT: G 271 MET cc_start: 0.8784 (mmp) cc_final: 0.8341 (mmm) REVERT: J 595 ILE cc_start: 0.9745 (tp) cc_final: 0.9299 (pt) REVERT: J 647 GLU cc_start: 0.9359 (tt0) cc_final: 0.8885 (tp30) REVERT: C 108 CYS cc_start: 0.7507 (t) cc_final: 0.6423 (t) REVERT: E 108 CYS cc_start: 0.7192 (t) cc_final: 0.6175 (t) REVERT: H 108 CYS cc_start: 0.7228 (t) cc_final: 0.6458 (t) outliers start: 2 outliers final: 1 residues processed: 222 average time/residue: 0.3535 time to fit residues: 115.3210 Evaluate side-chains 179 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 232 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 94 ASN A 130 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN G 130 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN D 194 GLN E 223 GLN H 223 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.085306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066556 restraints weight = 1942719.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068519 restraints weight = 456761.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.069555 restraints weight = 201919.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070091 restraints weight = 129461.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.070426 restraints weight = 105160.071| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1012 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1035 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 25947 Z= 0.278 Angle : 0.925 20.566 35679 Z= 0.426 Chirality : 0.052 0.895 4482 Planarity : 0.006 0.209 4272 Dihedral : 10.151 68.451 6252 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 37.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.46 % Allowed : 0.84 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3066 helix: 0.48 (0.25), residues: 411 sheet: 0.23 (0.14), residues: 1179 loop : 0.70 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 50 TYR 0.028 0.002 TYR G 217 PHE 0.028 0.003 PHE F 353 TRP 0.022 0.002 TRP A 45 HIS 0.009 0.003 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00569 (25737) covalent geometry : angle 0.83808 (35118) SS BOND : bond 0.00372 ( 60) SS BOND : angle 1.36487 ( 120) hydrogen bonds : bond 0.03802 ( 963) hydrogen bonds : angle 6.27406 ( 2556) Misc. bond : bond 0.01378 ( 3) link_ALPHA1-2 : bond 0.00196 ( 6) link_ALPHA1-2 : angle 2.01922 ( 18) link_ALPHA1-3 : bond 0.00472 ( 18) link_ALPHA1-3 : angle 1.94740 ( 54) link_ALPHA1-6 : bond 0.00890 ( 15) link_ALPHA1-6 : angle 2.89986 ( 45) link_BETA1-4 : bond 0.00715 ( 51) link_BETA1-4 : angle 2.56828 ( 153) link_NAG-ASN : bond 0.00973 ( 57) link_NAG-ASN : angle 4.83283 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8556 (OUTLIER) cc_final: 0.8011 (m-90) REVERT: A 100 MET cc_start: 0.9426 (ptp) cc_final: 0.9070 (ptp) REVERT: A 104 MET cc_start: 0.9601 (tmm) cc_final: 0.9294 (tmm) REVERT: A 114 GLN cc_start: 0.9720 (tp40) cc_final: 0.9288 (tm-30) REVERT: B 626 MET cc_start: 0.9241 (ptm) cc_final: 0.8801 (ttp) REVERT: B 647 GLU cc_start: 0.9304 (pt0) cc_final: 0.9097 (tp30) REVERT: F 69 TRP cc_start: 0.8859 (m100) cc_final: 0.8535 (m100) REVERT: F 100 MET cc_start: 0.9402 (ptp) cc_final: 0.9057 (ptp) REVERT: F 104 MET cc_start: 0.9615 (tmm) cc_final: 0.9230 (tmm) REVERT: G 35 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.6828 (m-90) REVERT: G 69 TRP cc_start: 0.8805 (m100) cc_final: 0.8499 (m100) REVERT: G 100 MET cc_start: 0.9406 (ptp) cc_final: 0.9136 (ptp) REVERT: G 271 MET cc_start: 0.8442 (mmp) cc_final: 0.8164 (mmm) REVERT: J 626 MET cc_start: 0.9244 (ptt) cc_final: 0.8815 (ppp) REVERT: C 108 CYS cc_start: 0.7030 (t) cc_final: 0.6471 (t) outliers start: 3 outliers final: 1 residues processed: 198 average time/residue: 0.3478 time to fit residues: 100.2682 Evaluate side-chains 163 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 190 optimal weight: 0.2980 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 0.0570 chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.087758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069106 restraints weight = 1855309.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.071154 restraints weight = 442179.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072206 restraints weight = 194380.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072822 restraints weight = 125025.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.073202 restraints weight = 100234.049| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1035 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1028 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25947 Z= 0.118 Angle : 0.661 19.742 35679 Z= 0.310 Chirality : 0.047 0.678 4482 Planarity : 0.004 0.125 4272 Dihedral : 9.425 65.866 6252 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.46 % Allowed : 0.69 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.15), residues: 3066 helix: 1.19 (0.26), residues: 414 sheet: 0.33 (0.14), residues: 1185 loop : 0.95 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 116 TYR 0.014 0.001 TYR H 198 PHE 0.014 0.001 PHE H 166 TRP 0.016 0.001 TRP J 628 HIS 0.004 0.001 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00242 (25737) covalent geometry : angle 0.57763 (35118) SS BOND : bond 0.00354 ( 60) SS BOND : angle 1.05005 ( 120) hydrogen bonds : bond 0.03267 ( 963) hydrogen bonds : angle 5.75030 ( 2556) Misc. bond : bond 0.01008 ( 3) link_ALPHA1-2 : bond 0.00220 ( 6) link_ALPHA1-2 : angle 1.70040 ( 18) link_ALPHA1-3 : bond 0.00607 ( 18) link_ALPHA1-3 : angle 1.62146 ( 54) link_ALPHA1-6 : bond 0.00868 ( 15) link_ALPHA1-6 : angle 2.17214 ( 45) link_BETA1-4 : bond 0.00354 ( 51) link_BETA1-4 : angle 1.98298 ( 153) link_NAG-ASN : bond 0.00288 ( 57) link_NAG-ASN : angle 4.00107 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8327 (m-90) cc_final: 0.8121 (m-90) REVERT: A 100 MET cc_start: 0.9414 (ptp) cc_final: 0.9024 (ptp) REVERT: A 104 MET cc_start: 0.9597 (tmm) cc_final: 0.9211 (tmm) REVERT: A 114 GLN cc_start: 0.9683 (tp40) cc_final: 0.9295 (tm-30) REVERT: A 150 MET cc_start: 0.8284 (mmm) cc_final: 0.8038 (mmm) REVERT: B 626 MET cc_start: 0.9233 (ptm) cc_final: 0.8807 (ttp) REVERT: B 647 GLU cc_start: 0.9240 (pt0) cc_final: 0.9010 (tp30) REVERT: F 100 MET cc_start: 0.9373 (ptp) cc_final: 0.9026 (ptp) REVERT: F 104 MET cc_start: 0.9632 (tmm) cc_final: 0.9209 (tmm) REVERT: F 150 MET cc_start: 0.8778 (mtm) cc_final: 0.8311 (mtm) REVERT: G 45 TRP cc_start: 0.7887 (m-90) cc_final: 0.7478 (m-90) REVERT: G 100 MET cc_start: 0.9389 (ptp) cc_final: 0.9074 (ptp) REVERT: G 150 MET cc_start: 0.8925 (mmm) cc_final: 0.8629 (mmm) REVERT: G 271 MET cc_start: 0.8739 (mmp) cc_final: 0.8346 (mmm) REVERT: J 626 MET cc_start: 0.9173 (ptt) cc_final: 0.8631 (ppp) REVERT: E 108 CYS cc_start: 0.5315 (t) cc_final: 0.4951 (t) REVERT: K 62 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9085 (mppt) REVERT: H 108 CYS cc_start: 0.5145 (t) cc_final: 0.4742 (t) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3233 time to fit residues: 90.7180 Evaluate side-chains 160 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN B 550 GLN B 640 GLN F 287 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 GLN ** I 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 640 GLN G 287 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN J 550 GLN ** J 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.081930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063049 restraints weight = 2049059.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065459 restraints weight = 472116.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066376 restraints weight = 206300.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.066875 restraints weight = 133143.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067107 restraints weight = 108965.568| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1028 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1077 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25947 Z= 0.326 Angle : 0.954 16.949 35679 Z= 0.446 Chirality : 0.049 0.645 4482 Planarity : 0.005 0.077 4272 Dihedral : 9.514 63.391 6252 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 51.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.46 % Allowed : 1.52 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3066 helix: -0.59 (0.23), residues: 423 sheet: 0.07 (0.14), residues: 1173 loop : 0.02 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 116 TYR 0.026 0.003 TYR I 643 PHE 0.030 0.004 PHE A 391 TRP 0.030 0.003 TRP A 45 HIS 0.011 0.004 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00655 (25737) covalent geometry : angle 0.89074 (35118) SS BOND : bond 0.00594 ( 60) SS BOND : angle 1.27587 ( 120) hydrogen bonds : bond 0.03820 ( 963) hydrogen bonds : angle 6.71898 ( 2556) Misc. bond : bond 0.00458 ( 3) link_ALPHA1-2 : bond 0.00267 ( 6) link_ALPHA1-2 : angle 2.15326 ( 18) link_ALPHA1-3 : bond 0.00284 ( 18) link_ALPHA1-3 : angle 2.03491 ( 54) link_ALPHA1-6 : bond 0.00883 ( 15) link_ALPHA1-6 : angle 2.37276 ( 45) link_BETA1-4 : bond 0.00721 ( 51) link_BETA1-4 : angle 2.41804 ( 153) link_NAG-ASN : bond 0.01226 ( 57) link_NAG-ASN : angle 4.14845 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9442 (ptp) cc_final: 0.9018 (ptp) REVERT: A 104 MET cc_start: 0.9590 (tmm) cc_final: 0.9289 (tmm) REVERT: A 150 MET cc_start: 0.8215 (mmm) cc_final: 0.7600 (mmm) REVERT: B 626 MET cc_start: 0.9217 (ptm) cc_final: 0.8533 (ttp) REVERT: B 647 GLU cc_start: 0.9436 (pt0) cc_final: 0.9051 (tp30) REVERT: F 100 MET cc_start: 0.9485 (ptp) cc_final: 0.9182 (ptp) REVERT: F 104 MET cc_start: 0.9617 (tmm) cc_final: 0.9303 (tmm) REVERT: F 161 MET cc_start: 0.9566 (tpp) cc_final: 0.9164 (tpt) REVERT: G 100 MET cc_start: 0.9554 (ptp) cc_final: 0.9160 (ptp) REVERT: G 150 MET cc_start: 0.8875 (mmm) cc_final: 0.8355 (mmm) REVERT: J 595 ILE cc_start: 0.9764 (tt) cc_final: 0.9342 (pt) REVERT: J 626 MET cc_start: 0.9222 (ptt) cc_final: 0.8627 (ppp) REVERT: J 647 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9110 (tp30) REVERT: C 108 CYS cc_start: 0.5893 (t) cc_final: 0.4339 (t) REVERT: E 108 CYS cc_start: 0.5432 (t) cc_final: 0.5067 (t) REVERT: H 108 CYS cc_start: 0.5851 (t) cc_final: 0.5588 (t) REVERT: L 62 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9146 (mppt) REVERT: L 76 ILE cc_start: 0.7777 (mm) cc_final: 0.7555 (mt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3319 time to fit residues: 84.6252 Evaluate side-chains 148 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 5 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 246 optimal weight: 0.0170 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.084651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066046 restraints weight = 1969470.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068099 restraints weight = 452366.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.069190 restraints weight = 199610.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.069698 restraints weight = 128436.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070124 restraints weight = 105386.320| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1077 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1067 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25947 Z= 0.143 Angle : 0.679 17.214 35679 Z= 0.318 Chirality : 0.047 0.607 4482 Planarity : 0.006 0.190 4272 Dihedral : 8.736 60.188 6252 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 37.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.46 % Allowed : 0.50 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3066 helix: 0.38 (0.26), residues: 408 sheet: 0.18 (0.14), residues: 1197 loop : 0.45 (0.18), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 116 TYR 0.021 0.001 TYR G 217 PHE 0.016 0.002 PHE H 166 TRP 0.017 0.001 TRP B 628 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00293 (25737) covalent geometry : angle 0.59856 (35118) SS BOND : bond 0.00175 ( 60) SS BOND : angle 1.13054 ( 120) hydrogen bonds : bond 0.03219 ( 963) hydrogen bonds : angle 6.05251 ( 2556) Misc. bond : bond 0.00882 ( 3) link_ALPHA1-2 : bond 0.00235 ( 6) link_ALPHA1-2 : angle 1.69552 ( 18) link_ALPHA1-3 : bond 0.00545 ( 18) link_ALPHA1-3 : angle 1.64659 ( 54) link_ALPHA1-6 : bond 0.00921 ( 15) link_ALPHA1-6 : angle 2.18283 ( 45) link_BETA1-4 : bond 0.00334 ( 51) link_BETA1-4 : angle 1.81823 ( 153) link_NAG-ASN : bond 0.00444 ( 57) link_NAG-ASN : angle 4.05704 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8600 (m-90) cc_final: 0.8312 (m-90) REVERT: A 104 MET cc_start: 0.9610 (tmm) cc_final: 0.9264 (tmm) REVERT: A 150 MET cc_start: 0.8430 (mmm) cc_final: 0.8007 (mmm) REVERT: B 647 GLU cc_start: 0.9368 (pt0) cc_final: 0.8998 (tp30) REVERT: F 45 TRP cc_start: 0.8060 (m-90) cc_final: 0.7628 (m-90) REVERT: F 104 MET cc_start: 0.9643 (tmm) cc_final: 0.9274 (tmm) REVERT: F 161 MET cc_start: 0.9575 (tpp) cc_final: 0.9082 (tpt) REVERT: G 45 TRP cc_start: 0.7979 (m-90) cc_final: 0.7419 (m-90) REVERT: G 150 MET cc_start: 0.9015 (mmm) cc_final: 0.8478 (mmm) REVERT: G 271 MET cc_start: 0.8651 (mmp) cc_final: 0.8395 (mmm) REVERT: J 626 MET cc_start: 0.9259 (ptt) cc_final: 0.8983 (ppp) REVERT: C 108 CYS cc_start: 0.4281 (t) cc_final: 0.3904 (t) REVERT: E 108 CYS cc_start: 0.5369 (t) cc_final: 0.4552 (t) REVERT: K 62 LYS cc_start: 0.9332 (mmmt) cc_final: 0.9012 (mppt) REVERT: H 108 CYS cc_start: 0.5185 (t) cc_final: 0.4496 (t) REVERT: L 62 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9171 (mppt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3317 time to fit residues: 89.1235 Evaluate side-chains 151 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 220 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.081884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063200 restraints weight = 1983754.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065304 restraints weight = 461791.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066290 restraints weight = 207209.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066811 restraints weight = 134856.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067240 restraints weight = 109074.290| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1067 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1093 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25947 Z= 0.264 Angle : 0.826 16.875 35679 Z= 0.385 Chirality : 0.049 0.843 4482 Planarity : 0.005 0.135 4272 Dihedral : 8.755 58.300 6252 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 48.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.46 % Allowed : 0.69 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3066 helix: -0.35 (0.24), residues: 423 sheet: 0.07 (0.14), residues: 1179 loop : -0.01 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 50 TYR 0.023 0.002 TYR G 217 PHE 0.024 0.003 PHE A 353 TRP 0.021 0.002 TRP A 45 HIS 0.007 0.002 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00527 (25737) covalent geometry : angle 0.75935 (35118) SS BOND : bond 0.00342 ( 60) SS BOND : angle 1.06005 ( 120) hydrogen bonds : bond 0.03454 ( 963) hydrogen bonds : angle 6.39654 ( 2556) Misc. bond : bond 0.00850 ( 3) link_ALPHA1-2 : bond 0.00137 ( 6) link_ALPHA1-2 : angle 1.87262 ( 18) link_ALPHA1-3 : bond 0.00373 ( 18) link_ALPHA1-3 : angle 1.80417 ( 54) link_ALPHA1-6 : bond 0.00846 ( 15) link_ALPHA1-6 : angle 2.25262 ( 45) link_BETA1-4 : bond 0.00621 ( 51) link_BETA1-4 : angle 2.13918 ( 153) link_NAG-ASN : bond 0.00834 ( 57) link_NAG-ASN : angle 4.04679 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9477 (ptp) cc_final: 0.9119 (ptp) REVERT: A 104 MET cc_start: 0.9585 (tmm) cc_final: 0.9256 (tmm) REVERT: A 150 MET cc_start: 0.8391 (mmm) cc_final: 0.7958 (mmm) REVERT: B 530 MET cc_start: 0.8690 (ttm) cc_final: 0.8183 (ttp) REVERT: B 647 GLU cc_start: 0.9433 (pt0) cc_final: 0.9037 (tp30) REVERT: F 100 MET cc_start: 0.9483 (ptp) cc_final: 0.9130 (ptp) REVERT: F 104 MET cc_start: 0.9630 (tmm) cc_final: 0.9271 (tmm) REVERT: F 161 MET cc_start: 0.9596 (tpp) cc_final: 0.9037 (tpt) REVERT: G 150 MET cc_start: 0.8956 (mmm) cc_final: 0.8382 (mmm) REVERT: J 530 MET cc_start: 0.8680 (ttm) cc_final: 0.8140 (ttp) REVERT: J 626 MET cc_start: 0.9314 (ptt) cc_final: 0.8861 (ppp) REVERT: C 108 CYS cc_start: 0.4506 (t) cc_final: 0.3980 (t) REVERT: E 108 CYS cc_start: 0.5504 (t) cc_final: 0.4963 (t) REVERT: H 108 CYS cc_start: 0.5349 (t) cc_final: 0.4908 (t) REVERT: L 62 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9201 (mppt) REVERT: L 76 ILE cc_start: 0.7867 (mm) cc_final: 0.7625 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3375 time to fit residues: 79.1947 Evaluate side-chains 144 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 159 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN L 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.081541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063323 restraints weight = 1932407.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065532 restraints weight = 462957.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066364 restraints weight = 203053.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067171 restraints weight = 128115.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067112 restraints weight = 93863.642| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1093 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25947 Z= 0.255 Angle : 0.795 17.450 35679 Z= 0.376 Chirality : 0.049 0.890 4482 Planarity : 0.005 0.108 4272 Dihedral : 8.687 59.462 6252 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 49.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.02 % Favored : 92.94 % Rotamer: Outliers : 0.46 % Allowed : 0.30 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3066 helix: -0.77 (0.23), residues: 444 sheet: 0.07 (0.15), residues: 1143 loop : -0.24 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 116 TYR 0.028 0.002 TYR L 79 PHE 0.022 0.003 PHE G 233 TRP 0.024 0.002 TRP A 45 HIS 0.008 0.002 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00506 (25737) covalent geometry : angle 0.72641 (35118) SS BOND : bond 0.00250 ( 60) SS BOND : angle 1.02700 ( 120) hydrogen bonds : bond 0.03470 ( 963) hydrogen bonds : angle 6.48339 ( 2556) Misc. bond : bond 0.00640 ( 3) link_ALPHA1-2 : bond 0.00131 ( 6) link_ALPHA1-2 : angle 1.75431 ( 18) link_ALPHA1-3 : bond 0.00420 ( 18) link_ALPHA1-3 : angle 1.72184 ( 54) link_ALPHA1-6 : bond 0.00926 ( 15) link_ALPHA1-6 : angle 2.19838 ( 45) link_BETA1-4 : bond 0.00575 ( 51) link_BETA1-4 : angle 2.02348 ( 153) link_NAG-ASN : bond 0.00683 ( 57) link_NAG-ASN : angle 4.07906 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8762 (m-90) cc_final: 0.8524 (m-90) REVERT: A 104 MET cc_start: 0.9585 (tmm) cc_final: 0.9253 (tmm) REVERT: A 150 MET cc_start: 0.8554 (mmm) cc_final: 0.8011 (mmm) REVERT: B 530 MET cc_start: 0.8694 (ttm) cc_final: 0.8159 (ttp) REVERT: B 647 GLU cc_start: 0.9500 (pt0) cc_final: 0.9025 (tp30) REVERT: F 104 MET cc_start: 0.9613 (tmm) cc_final: 0.9244 (tmm) REVERT: F 161 MET cc_start: 0.9618 (tpp) cc_final: 0.9101 (tpt) REVERT: I 530 MET cc_start: 0.9147 (ttm) cc_final: 0.8743 (ttm) REVERT: G 150 MET cc_start: 0.8959 (mmm) cc_final: 0.8405 (mmm) REVERT: G 271 MET cc_start: 0.8751 (mmp) cc_final: 0.8548 (mmm) REVERT: J 530 MET cc_start: 0.8711 (ttm) cc_final: 0.8208 (ttp) REVERT: J 626 MET cc_start: 0.9316 (ptt) cc_final: 0.8997 (ppp) REVERT: C 108 CYS cc_start: 0.5112 (t) cc_final: 0.4202 (t) REVERT: E 108 CYS cc_start: 0.5353 (t) cc_final: 0.4917 (t) REVERT: K 62 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9288 (mppt) REVERT: H 108 CYS cc_start: 0.5198 (t) cc_final: 0.4883 (t) REVERT: L 62 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9171 (mppt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3375 time to fit residues: 80.0140 Evaluate side-chains 136 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 158 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.082498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064538 restraints weight = 2036561.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066788 restraints weight = 476751.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067732 restraints weight = 213499.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068246 restraints weight = 124607.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068263 restraints weight = 98951.825| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25947 Z= 0.176 Angle : 0.692 13.864 35679 Z= 0.326 Chirality : 0.047 0.822 4482 Planarity : 0.004 0.092 4272 Dihedral : 8.267 59.880 6252 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 44.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.46 % Allowed : 0.19 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3066 helix: -0.13 (0.25), residues: 426 sheet: 0.14 (0.15), residues: 1143 loop : -0.10 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 50 TYR 0.023 0.001 TYR E 198 PHE 0.033 0.002 PHE A 233 TRP 0.015 0.002 TRP I 596 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd covalent geometry : bond 0.00352 (25737) covalent geometry : angle 0.62255 (35118) SS BOND : bond 0.00199 ( 60) SS BOND : angle 0.96665 ( 120) hydrogen bonds : bond 0.03185 ( 963) hydrogen bonds : angle 6.12261 ( 2556) Misc. bond : bond 0.00708 ( 3) link_ALPHA1-2 : bond 0.00212 ( 6) link_ALPHA1-2 : angle 1.68162 ( 18) link_ALPHA1-3 : bond 0.00483 ( 18) link_ALPHA1-3 : angle 1.60383 ( 54) link_ALPHA1-6 : bond 0.00872 ( 15) link_ALPHA1-6 : angle 2.08358 ( 45) link_BETA1-4 : bond 0.00446 ( 51) link_BETA1-4 : angle 1.84957 ( 153) link_NAG-ASN : bond 0.00520 ( 57) link_NAG-ASN : angle 3.77146 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8679 (m-90) cc_final: 0.8412 (m-90) REVERT: A 104 MET cc_start: 0.9589 (tmm) cc_final: 0.9228 (tmm) REVERT: A 150 MET cc_start: 0.8743 (mmm) cc_final: 0.8271 (mmm) REVERT: B 647 GLU cc_start: 0.9460 (pt0) cc_final: 0.9030 (tp30) REVERT: F 104 MET cc_start: 0.9613 (tmm) cc_final: 0.9233 (tmm) REVERT: F 161 MET cc_start: 0.9583 (tpp) cc_final: 0.9095 (tpt) REVERT: I 530 MET cc_start: 0.9134 (ttm) cc_final: 0.8688 (ttp) REVERT: G 150 MET cc_start: 0.9046 (mmm) cc_final: 0.8549 (mmm) REVERT: J 626 MET cc_start: 0.9345 (ptt) cc_final: 0.8716 (ptm) REVERT: C 108 CYS cc_start: 0.4884 (t) cc_final: 0.4159 (t) REVERT: E 108 CYS cc_start: 0.4716 (t) cc_final: 0.4487 (t) REVERT: H 108 CYS cc_start: 0.4687 (t) cc_final: 0.4399 (t) REVERT: L 62 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9195 (mppt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3414 time to fit residues: 80.9679 Evaluate side-chains 139 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 117 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 53 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.083190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065354 restraints weight = 1911199.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067454 restraints weight = 454756.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.068527 restraints weight = 192126.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069174 restraints weight = 117596.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069245 restraints weight = 89950.099| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25947 Z= 0.133 Angle : 0.637 13.576 35679 Z= 0.300 Chirality : 0.046 0.692 4482 Planarity : 0.004 0.081 4272 Dihedral : 7.764 59.685 6252 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 41.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.46 % Allowed : 0.11 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 3066 helix: 0.16 (0.25), residues: 444 sheet: 0.16 (0.15), residues: 1167 loop : 0.14 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 50 TYR 0.019 0.001 TYR G 217 PHE 0.013 0.001 PHE H 166 TRP 0.019 0.001 TRP B 623 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00270 (25737) covalent geometry : angle 0.56722 (35118) SS BOND : bond 0.00184 ( 60) SS BOND : angle 0.97166 ( 120) hydrogen bonds : bond 0.02995 ( 963) hydrogen bonds : angle 5.81899 ( 2556) Misc. bond : bond 0.00616 ( 3) link_ALPHA1-2 : bond 0.00264 ( 6) link_ALPHA1-2 : angle 1.64525 ( 18) link_ALPHA1-3 : bond 0.00528 ( 18) link_ALPHA1-3 : angle 1.56487 ( 54) link_ALPHA1-6 : bond 0.00842 ( 15) link_ALPHA1-6 : angle 1.82469 ( 45) link_BETA1-4 : bond 0.00395 ( 51) link_BETA1-4 : angle 1.79519 ( 153) link_NAG-ASN : bond 0.00351 ( 57) link_NAG-ASN : angle 3.62226 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7703.80 seconds wall clock time: 132 minutes 49.12 seconds (7969.12 seconds total)