Starting phenix.real_space_refine on Tue Sep 15 17:50:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_7896.cif Found real_map, /net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_7896.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_7896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_7896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_7896.map" model { file = "/net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_7896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6did_7896/09_2026/6did_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 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 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 chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 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 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 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 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 chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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 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 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 chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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 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 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 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 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 chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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 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 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 chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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: 8.18, per 1000 atoms: 0.24 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: 3.70 Conformation dependent library (CDL) restraints added in 1.7 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: 0.80 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: 9.39 Time building geometry restraints manager: 4.70 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 - 17.62: 16855 17.62 - 35.25: 704 35.25 - 52.87: 216 52.87 - 70.49: 111 70.49 - 88.11: 9 Dihedral angle restraints: 17895 sinusoidal: 8511 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 17892 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: 0.08 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.310 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.550 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.160 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 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 : 11.524 88.113 8544 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/Z covalent geometry : bond 0.01404 / 0.82 (25737) covalent geometry : angle 1.60682 / 0.97 (35118) SS BOND : bond 0.04124 / 2.41 ( 60) SS BOND : angle 2.62167 / 1.76 ( 120) hydrogen bonds : bond 0.15859 / 10.71 ( 963) hydrogen bonds : angle 8.16273 / 5.78 ( 2556) Misc. bond : bond 0.60943 / 30.48 ( 3) link_ALPHA1-2 : bond 0.02124 / 1.28 ( 6) link_ALPHA1-2 : angle 3.75098 / 2.35 ( 18) link_ALPHA1-3 : bond 0.03206 / 2.01 ( 18) link_ALPHA1-3 : angle 3.20075 / 2.27 ( 54) link_ALPHA1-6 : bond 0.02864 / 1.78 ( 15) link_ALPHA1-6 : angle 6.75122 / 4.65 ( 45) link_BETA1-4 : bond 0.02973 / 1.74 ( 51) link_BETA1-4 : angle 4.98248 / 3.37 ( 153) link_NAG-ASN : bond 0.02753 / 1.64 ( 57) link_NAG-ASN : angle 11.17192 / 7.93 ( 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 : 1.249 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: 0.9528 (mm) REVERT: G 475 MET cc_start: 0.8822 (mmp) cc_final: 0.8424 (mmm) REVERT: J 536 THR cc_start: 0.9066 (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: 0.6824 (t) REVERT: H 89 THR cc_start: 0.6076 (OUTLIER) cc_final: 0.5688 (t) REVERT: H 149 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7159 (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: 0.2858 time to fit residues: 164.8290 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 : 1.231 ------------------------------------------------------------------------------- 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... A 80 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.090802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.072261 restraints weight = 1737474.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.074918 restraints weight = 439925.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.075866 restraints weight = 180586.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.076411 restraints weight = 121075.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.076544 restraints weight = 93980.966| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 630 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1036 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25947 Z= 0.215 Angle : 0.892 18.040 35679 Z= 0.423 Chirality : 0.046 0.220 4482 Planarity : 0.007 0.218 4272 Dihedral : 6.172 33.526 3273 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.30 % Allowed : 1.10 % Favored : 98.59 % 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: 0.50 (0.14), residues: 1215 loop : 1.48 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG E 50 TYR 0.025 0.002 TYR E 52 PHE 0.019 0.002 PHE F 353 TRP 0.024 0.002 TRP F 69 HIS 0.011 0.002 HIS F 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (25737) covalent geometry : angle 0.78816 / 0.40 (35118) SS BOND : bond 0.00426 / 0.29 ( 60) SS BOND : angle 2.07902 / 1.27 ( 120) hydrogen bonds : bond 0.04723 / 3.17 ( 963) hydrogen bonds : angle 6.67697 / 4.73 ( 2556) Misc. bond : bond 0.00828 / 0.41 ( 3) link_ALPHA1-2 : bond 0.00102 / 0.06 ( 6) link_ALPHA1-2 : angle 1.99862 / 1.21 ( 18) link_ALPHA1-3 : bond 0.00307 / 0.19 ( 18) link_ALPHA1-3 : angle 1.68316 / 1.16 ( 54) link_ALPHA1-6 : bond 0.00321 / 0.17 ( 15) link_ALPHA1-6 : angle 1.68306 / 1.14 ( 45) link_BETA1-4 : bond 0.00501 / 0.28 ( 51) link_BETA1-4 : angle 2.34088 / 1.64 ( 153) link_NAG-ASN : bond 0.00566 / 0.36 ( 57) link_NAG-ASN : angle 5.32957 / 3.86 ( 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 251 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 246 time to evaluate : 1.137 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: A 45 TRP cc_start: 0.8248 (m-90) cc_final: 0.8001 (m-90) REVERT: A 104 MET cc_start: 0.9410 (tmm) cc_final: 0.9151 (ppp) REVERT: A 107 ASP cc_start: 0.9476 (t70) cc_final: 0.8967 (t0) REVERT: A 114 GLN cc_start: 0.9648 (tp40) cc_final: 0.9226 (tm-30) REVERT: B 647 GLU cc_start: 0.8834 (tt0) cc_final: 0.8531 (tt0) REVERT: F 69 TRP cc_start: 0.8692 (m100) cc_final: 0.8274 (m100) REVERT: F 104 MET cc_start: 0.9444 (tmm) cc_final: 0.9207 (ppp) REVERT: F 107 ASP cc_start: 0.9369 (t70) cc_final: 0.8957 (t0) REVERT: I 647 GLU cc_start: 0.9017 (tt0) cc_final: 0.8696 (tt0) REVERT: G 45 TRP cc_start: 0.8156 (m-90) cc_final: 0.7905 (m-90) REVERT: G 69 TRP cc_start: 0.8769 (m100) cc_final: 0.8370 (m100) REVERT: G 161 MET cc_start: 0.9243 (tmm) cc_final: 0.9027 (tmm) REVERT: C 108 CYS cc_start: 0.7932 (t) cc_final: 0.6225 (m) REVERT: D 76 ILE cc_start: 0.7700 (mm) cc_final: 0.7487 (mt) REVERT: E 108 CYS cc_start: 0.7910 (t) cc_final: 0.6226 (m) REVERT: H 108 CYS cc_start: 0.8258 (t) cc_final: 0.6811 (m) outliers start: 5 outliers final: 0 residues processed: 251 average time/residue: 0.3040 time to fit residues: 115.2876 Evaluate side-chains 191 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 8.9990 chunk 27 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** 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 170 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.064667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044022 restraints weight = 1523716.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046396 restraints weight = 390992.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047939 restraints weight = 185832.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048981 restraints weight = 115751.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049597 restraints weight = 84236.592| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1036 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 950 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25947 Z= 0.231 Angle : 0.850 23.030 35679 Z= 0.402 Chirality : 0.052 1.034 4482 Planarity : 0.005 0.122 4272 Dihedral : 5.621 35.506 3273 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.42 % Allowed : 1.83 % Favored : 97.75 % 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: 1.00 (0.15), residues: 3066 helix: 1.04 (0.26), residues: 411 sheet: 0.30 (0.14), residues: 1182 loop : 1.12 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 50 TYR 0.025 0.002 TYR G 217 PHE 0.026 0.003 PHE D 145 TRP 0.018 0.002 TRP G 395 HIS 0.008 0.002 HIS F 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (25737) covalent geometry : angle 0.75834 / 0.38 (35118) SS BOND : bond 0.00657 / 0.46 ( 60) SS BOND : angle 2.05537 / 1.32 ( 120) hydrogen bonds : bond 0.03904 / 2.57 ( 963) hydrogen bonds : angle 6.27071 / 4.46 ( 2556) Misc. bond : bond 0.01241 / 0.62 ( 3) link_ALPHA1-2 : bond 0.00053 / 0.03 ( 6) link_ALPHA1-2 : angle 1.94919 / 1.22 ( 18) link_ALPHA1-3 : bond 0.00192 / 0.11 ( 18) link_ALPHA1-3 : angle 1.67020 / 1.13 ( 54) link_ALPHA1-6 : bond 0.00653 / 0.34 ( 15) link_ALPHA1-6 : angle 1.88318 / 1.29 ( 45) link_BETA1-4 : bond 0.00517 / 0.31 ( 51) link_BETA1-4 : angle 2.29953 / 1.78 ( 153) link_NAG-ASN : bond 0.01071 / 0.76 ( 57) link_NAG-ASN : angle 4.76732 / 3.51 ( 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 216 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.969 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: A 45 TRP cc_start: 0.8268 (m-90) cc_final: 0.7949 (m-90) REVERT: A 114 GLN cc_start: 0.9703 (tp40) cc_final: 0.9323 (tm-30) REVERT: A 150 MET cc_start: 0.8452 (mmm) cc_final: 0.7743 (mmm) REVERT: B 626 MET cc_start: 0.9219 (ptm) cc_final: 0.8908 (ttp) REVERT: F 45 TRP cc_start: 0.8169 (m-90) cc_final: 0.7813 (m-90) REVERT: F 69 TRP cc_start: 0.8724 (m100) cc_final: 0.8348 (m100) REVERT: F 104 MET cc_start: 0.9470 (tmm) cc_final: 0.9227 (tmm) REVERT: F 462 ASN cc_start: 0.8979 (m-40) cc_final: 0.8739 (t0) REVERT: I 626 MET cc_start: 0.9240 (ptm) cc_final: 0.8994 (ttp) REVERT: G 45 TRP cc_start: 0.8137 (m-90) cc_final: 0.7828 (m-90) REVERT: G 69 TRP cc_start: 0.8749 (m100) cc_final: 0.8380 (m100) REVERT: G 195 ASN cc_start: 0.9587 (p0) cc_final: 0.9254 (p0) REVERT: G 271 MET cc_start: 0.8961 (mmp) cc_final: 0.8548 (mmm) REVERT: J 595 ILE cc_start: 0.9740 (tp) cc_final: 0.9344 (pt) REVERT: J 647 GLU cc_start: 0.9508 (tt0) cc_final: 0.9034 (tp30) REVERT: C 108 CYS cc_start: 0.6853 (t) cc_final: 0.5301 (t) REVERT: D 145 PHE cc_start: 0.7491 (m-10) cc_final: 0.7106 (m-80) REVERT: E 108 CYS cc_start: 0.7161 (t) cc_final: 0.5783 (t) REVERT: K 145 PHE cc_start: 0.7868 (m-80) cc_final: 0.7612 (m-80) outliers start: 2 outliers final: 2 residues processed: 216 average time/residue: 0.2773 time to fit residues: 90.0391 Evaluate side-chains 180 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 3.9990 chunk 210 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 130 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN B 550 GLN B 590 GLN B 640 GLN F 82 GLN F 130 GLN F 287 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN I 550 GLN I 640 GLN G 82 GLN G 130 GLN ** G 287 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 550 GLN J 640 GLN C 223 GLN E 223 GLN H 223 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.081687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.063151 restraints weight = 1982424.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064988 restraints weight = 478222.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.065998 restraints weight = 211277.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066511 restraints weight = 134910.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066798 restraints weight = 109412.477| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 950 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1019 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 25947 Z= 0.392 Angle : 1.126 19.475 35679 Z= 0.524 Chirality : 0.053 0.822 4482 Planarity : 0.007 0.203 4272 Dihedral : 6.319 32.138 3273 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 55.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 0.61 % Allowed : 1.64 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.47 (0.15), residues: 3066 helix: -0.99 (0.23), residues: 423 sheet: -0.11 (0.14), residues: 1185 loop : -0.10 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 116 TYR 0.032 0.003 TYR G 217 PHE 0.035 0.004 PHE A 391 TRP 0.031 0.003 TRP A 395 HIS 0.014 0.004 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.39 (25737) covalent geometry : angle 1.04973 / 0.51 (35118) SS BOND : bond 0.00526 / 0.34 ( 60) SS BOND : angle 1.80680 / 1.20 ( 120) hydrogen bonds : bond 0.04405 / 2.94 ( 963) hydrogen bonds : angle 7.16190 / 5.08 ( 2556) Misc. bond : bond 0.01611 / 0.81 ( 3) link_ALPHA1-2 : bond 0.00319 / 0.19 ( 6) link_ALPHA1-2 : angle 2.31083 / 1.27 ( 18) link_ALPHA1-3 : bond 0.00294 / 0.18 ( 18) link_ALPHA1-3 : angle 1.88941 / 1.25 ( 54) link_ALPHA1-6 : bond 0.00510 / 0.27 ( 15) link_ALPHA1-6 : angle 1.87912 / 1.26 ( 45) link_BETA1-4 : bond 0.01051 / 0.63 ( 51) link_BETA1-4 : angle 2.81605 / 2.05 ( 153) link_NAG-ASN : bond 0.01388 / 0.86 ( 57) link_NAG-ASN : angle 5.12411 / 3.69 ( 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 189 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.955 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: A 100 MET cc_start: 0.9529 (ptp) cc_final: 0.9187 (ptp) REVERT: A 104 MET cc_start: 0.9694 (tmm) cc_final: 0.9468 (ppp) REVERT: A 150 MET cc_start: 0.8303 (mmm) cc_final: 0.7763 (mmm) REVERT: B 647 GLU cc_start: 0.9384 (pt0) cc_final: 0.9147 (tp30) REVERT: F 104 MET cc_start: 0.9629 (tmm) cc_final: 0.9404 (ppp) REVERT: F 462 ASN cc_start: 0.9063 (m-40) cc_final: 0.8828 (t0) REVERT: I 626 MET cc_start: 0.9365 (ptm) cc_final: 0.8990 (ptp) REVERT: G 100 MET cc_start: 0.9557 (ptp) cc_final: 0.9147 (ptp) REVERT: G 150 MET cc_start: 0.8743 (mmm) cc_final: 0.8105 (mmm) REVERT: G 271 MET cc_start: 0.8641 (mmp) cc_final: 0.8385 (mmm) REVERT: C 108 CYS cc_start: 0.7513 (t) cc_final: 0.6818 (t) REVERT: H 108 CYS cc_start: 0.8450 (t) cc_final: 0.5737 (t) outliers start: 4 outliers final: 0 residues processed: 189 average time/residue: 0.2984 time to fit residues: 84.1189 Evaluate side-chains 156 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 0.9980 chunk 103 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 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 = 0.3787 r_free = 0.3787 target = 0.085196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066799 restraints weight = 1887570.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.068373 restraints weight = 445487.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.069426 restraints weight = 199114.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.069945 restraints weight = 128694.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.070467 restraints weight = 105832.112| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1019 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1033 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25947 Z= 0.137 Angle : 0.688 18.387 35679 Z= 0.329 Chirality : 0.044 0.469 4482 Planarity : 0.005 0.133 4272 Dihedral : 5.455 33.764 3273 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 37.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.46 % Allowed : 0.76 % Favored : 98.78 % 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: 0.34 (0.15), residues: 3066 helix: 0.51 (0.26), residues: 390 sheet: 0.21 (0.14), residues: 1152 loop : 0.33 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 50 TYR 0.018 0.001 TYR G 217 PHE 0.016 0.002 PHE H 166 TRP 0.020 0.001 TRP I 628 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (25737) covalent geometry : angle 0.61600 / 0.31 (35118) SS BOND : bond 0.00509 / 0.28 ( 60) SS BOND : angle 1.06800 / 0.69 ( 120) hydrogen bonds : bond 0.03520 / 2.30 ( 963) hydrogen bonds : angle 6.30043 / 4.48 ( 2556) Misc. bond : bond 0.00652 / 0.33 ( 3) link_ALPHA1-2 : bond 0.00132 / 0.06 ( 6) link_ALPHA1-2 : angle 1.66754 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00260 / 0.15 ( 18) link_ALPHA1-3 : angle 1.57668 / 1.06 ( 54) link_ALPHA1-6 : bond 0.00567 / 0.30 ( 15) link_ALPHA1-6 : angle 1.72619 / 1.17 ( 45) link_BETA1-4 : bond 0.00387 / 0.24 ( 51) link_BETA1-4 : angle 1.84745 / 1.34 ( 153) link_NAG-ASN : bond 0.00464 / 0.31 ( 57) link_NAG-ASN : angle 3.87816 / 2.85 ( 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 189 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.165 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 45 TRP cc_start: 0.8340 (m-90) cc_final: 0.7930 (m-90) REVERT: A 104 MET cc_start: 0.9565 (tmm) cc_final: 0.9322 (ppp) REVERT: A 150 MET cc_start: 0.8466 (mmm) cc_final: 0.7976 (mmm) REVERT: A 161 MET cc_start: 0.9165 (tmm) cc_final: 0.8741 (tmm) REVERT: B 626 MET cc_start: 0.9403 (ptm) cc_final: 0.8806 (ttp) REVERT: B 647 GLU cc_start: 0.9309 (pt0) cc_final: 0.9020 (tp30) REVERT: F 104 MET cc_start: 0.9599 (tmm) cc_final: 0.9254 (tmm) REVERT: I 626 MET cc_start: 0.9357 (ptm) cc_final: 0.8890 (ttp) REVERT: I 647 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8962 (tp30) REVERT: G 150 MET cc_start: 0.8757 (mmm) cc_final: 0.8262 (mmm) REVERT: G 195 ASN cc_start: 0.9557 (p0) cc_final: 0.9299 (p0) REVERT: G 271 MET cc_start: 0.8762 (mmp) cc_final: 0.8434 (mmm) REVERT: J 595 ILE cc_start: 0.9825 (tp) cc_final: 0.9151 (pt) REVERT: J 647 GLU cc_start: 0.9371 (pt0) cc_final: 0.9151 (tp30) REVERT: D 62 LYS cc_start: 0.9430 (mmmt) cc_final: 0.9112 (mppt) REVERT: E 108 CYS cc_start: 0.5528 (t) cc_final: 0.4818 (t) REVERT: K 62 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9056 (mppt) REVERT: L 62 LYS cc_start: 0.9390 (mmmt) cc_final: 0.9106 (mppt) REVERT: L 76 ILE cc_start: 0.7805 (mm) cc_final: 0.7524 (mt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3057 time to fit residues: 86.1423 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 : 1.086 ------------------------------------------------------------------------------- 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: 0.8980 chunk 117 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 0.0020 chunk 251 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** G 328 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.084376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065755 restraints weight = 2008793.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068134 restraints weight = 465176.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.069171 restraints weight = 200887.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.069801 restraints weight = 127263.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.069864 restraints weight = 96238.084| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1033 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1039 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25947 Z= 0.173 Angle : 0.669 16.361 35679 Z= 0.321 Chirality : 0.043 0.398 4482 Planarity : 0.004 0.088 4272 Dihedral : 5.137 29.679 3273 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 39.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.46 % Allowed : 1.07 % Favored : 98.48 % 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: 0.35 (0.15), residues: 3066 helix: 0.76 (0.26), residues: 390 sheet: 0.11 (0.14), residues: 1194 loop : 0.38 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 50 TYR 0.021 0.002 TYR G 217 PHE 0.017 0.002 PHE F 159 TRP 0.014 0.001 TRP B 628 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (25737) covalent geometry : angle 0.60546 / 0.31 (35118) SS BOND : bond 0.00365 / 0.23 ( 60) SS BOND : angle 1.00062 / 0.64 ( 120) hydrogen bonds : bond 0.03222 / 2.11 ( 963) hydrogen bonds : angle 6.08117 / 4.34 ( 2556) Misc. bond : bond 0.00600 / 0.30 ( 3) link_ALPHA1-2 : bond 0.00114 / 0.05 ( 6) link_ALPHA1-2 : angle 1.72212 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00210 / 0.13 ( 18) link_ALPHA1-3 : angle 1.55585 / 1.06 ( 54) link_ALPHA1-6 : bond 0.00536 / 0.29 ( 15) link_ALPHA1-6 : angle 1.70848 / 1.16 ( 45) link_BETA1-4 : bond 0.00432 / 0.26 ( 51) link_BETA1-4 : angle 1.70682 / 1.24 ( 153) link_NAG-ASN : bond 0.00558 / 0.36 ( 57) link_NAG-ASN : angle 3.59090 / 2.62 ( 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 176 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.938 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 45 TRP cc_start: 0.8357 (m-90) cc_final: 0.7961 (m-90) REVERT: A 104 MET cc_start: 0.9563 (tmm) cc_final: 0.9238 (tmm) REVERT: A 150 MET cc_start: 0.8449 (mmm) cc_final: 0.7990 (mmm) REVERT: B 530 MET cc_start: 0.8659 (ttm) cc_final: 0.8291 (ttm) REVERT: B 626 MET cc_start: 0.9401 (ptm) cc_final: 0.8828 (ttp) REVERT: B 647 GLU cc_start: 0.9371 (pt0) cc_final: 0.9012 (tp30) REVERT: F 100 MET cc_start: 0.9546 (ptp) cc_final: 0.9197 (ptp) REVERT: F 104 MET cc_start: 0.9610 (tmm) cc_final: 0.9272 (tmm) REVERT: F 161 MET cc_start: 0.9514 (tpt) cc_final: 0.9270 (tpt) REVERT: F 462 ASN cc_start: 0.9025 (m-40) cc_final: 0.8780 (t0) REVERT: I 530 MET cc_start: 0.8537 (ttm) cc_final: 0.8230 (ttm) REVERT: I 626 MET cc_start: 0.9335 (ptm) cc_final: 0.8910 (ttp) REVERT: I 647 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8999 (tp30) REVERT: G 150 MET cc_start: 0.8704 (mmm) cc_final: 0.8207 (mmm) REVERT: G 195 ASN cc_start: 0.9575 (p0) cc_final: 0.9260 (p0) REVERT: G 271 MET cc_start: 0.8703 (mmp) cc_final: 0.8394 (mmm) REVERT: D 62 LYS cc_start: 0.9532 (mmmt) cc_final: 0.9263 (mppt) REVERT: E 108 CYS cc_start: 0.5065 (t) cc_final: 0.4511 (t) REVERT: K 62 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9149 (mppt) REVERT: L 62 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9184 (mppt) REVERT: L 76 ILE cc_start: 0.7705 (mm) cc_final: 0.7450 (mt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3057 time to fit residues: 80.6193 Evaluate side-chains 157 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 6.9990 chunk 241 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 overall best weight: 7.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 99 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.079928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061712 restraints weight = 2001845.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063460 restraints weight = 490346.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064385 restraints weight = 215560.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065236 restraints weight = 137085.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065159 restraints weight = 98833.677| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1039 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1055 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 25947 Z= 0.373 Angle : 0.999 15.072 35679 Z= 0.470 Chirality : 0.047 0.378 4482 Planarity : 0.006 0.172 4272 Dihedral : 5.973 36.722 3273 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 59.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 0.46 % Allowed : 2.21 % Favored : 97.33 % 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: -0.86 (0.15), residues: 3066 helix: -1.41 (0.22), residues: 444 sheet: -0.15 (0.15), residues: 1146 loop : -0.49 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 50 TYR 0.025 0.003 TYR G 217 PHE 0.032 0.004 PHE A 159 TRP 0.024 0.002 TRP F 395 HIS 0.011 0.004 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.37 (25737) covalent geometry : angle 0.94006 / 0.46 (35118) SS BOND : bond 0.00374 / 0.23 ( 60) SS BOND : angle 1.04994 / 0.73 ( 120) hydrogen bonds : bond 0.03997 / 2.65 ( 963) hydrogen bonds : angle 7.03605 / 5.00 ( 2556) Misc. bond : bond 0.01528 / 0.77 ( 3) link_ALPHA1-2 : bond 0.00272 / 0.16 ( 6) link_ALPHA1-2 : angle 2.25991 / 1.28 ( 18) link_ALPHA1-3 : bond 0.00258 / 0.16 ( 18) link_ALPHA1-3 : angle 1.86171 / 1.27 ( 54) link_ALPHA1-6 : bond 0.00603 / 0.32 ( 15) link_ALPHA1-6 : angle 1.80271 / 1.21 ( 45) link_BETA1-4 : bond 0.00861 / 0.51 ( 51) link_BETA1-4 : angle 2.41239 / 1.79 ( 153) link_NAG-ASN : bond 0.01212 / 0.77 ( 57) link_NAG-ASN : angle 4.28003 / 3.06 ( 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 158 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.104 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: A 100 MET cc_start: 0.9606 (ptp) cc_final: 0.9303 (ptp) REVERT: A 150 MET cc_start: 0.8362 (mmm) cc_final: 0.7934 (mmm) REVERT: B 530 MET cc_start: 0.8751 (ttm) cc_final: 0.8204 (ttp) REVERT: B 647 GLU cc_start: 0.9514 (pt0) cc_final: 0.9083 (tp30) REVERT: F 100 MET cc_start: 0.9547 (ptp) cc_final: 0.9123 (ptp) REVERT: F 104 MET cc_start: 0.9621 (tmm) cc_final: 0.9373 (ppp) REVERT: F 161 MET cc_start: 0.9528 (tpt) cc_final: 0.9277 (tpp) REVERT: I 530 MET cc_start: 0.8708 (ttm) cc_final: 0.8157 (ttp) REVERT: I 647 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9174 (tp30) REVERT: G 150 MET cc_start: 0.8736 (mmm) cc_final: 0.8152 (mmm) REVERT: J 530 MET cc_start: 0.9378 (ttm) cc_final: 0.8934 (ptm) REVERT: J 595 ILE cc_start: 0.9866 (tt) cc_final: 0.9018 (pt) REVERT: J 647 GLU cc_start: 0.9517 (pt0) cc_final: 0.9123 (tp30) REVERT: C 108 CYS cc_start: 0.5596 (t) cc_final: 0.5037 (t) REVERT: D 62 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9163 (mppt) REVERT: E 108 CYS cc_start: 0.5883 (t) cc_final: 0.5656 (t) REVERT: K 62 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9195 (mppt) REVERT: H 108 CYS cc_start: 0.5759 (t) cc_final: 0.5498 (t) REVERT: L 62 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9142 (mppt) REVERT: L 76 ILE cc_start: 0.8028 (mm) cc_final: 0.7795 (mt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3295 time to fit residues: 77.0068 Evaluate side-chains 141 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 10.0000 chunk 147 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** 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 99 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** 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 = 0.3691 r_free = 0.3691 target = 0.081504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063457 restraints weight = 1996718.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.065597 restraints weight = 480450.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.066492 restraints weight = 227906.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067328 restraints weight = 137110.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067003 restraints weight = 109321.776| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1055 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25947 Z= 0.244 Angle : 0.771 14.007 35679 Z= 0.368 Chirality : 0.046 0.563 4482 Planarity : 0.005 0.132 4272 Dihedral : 5.537 31.983 3273 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 50.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.46 % Allowed : 1.03 % Favored : 98.51 % 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: -0.72 (0.15), residues: 3066 helix: -1.07 (0.23), residues: 444 sheet: -0.09 (0.15), residues: 1143 loop : -0.46 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 50 TYR 0.020 0.002 TYR G 217 PHE 0.020 0.003 PHE A 353 TRP 0.032 0.002 TRP A 35 HIS 0.007 0.002 HIS F 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (25737) covalent geometry : angle 0.70236 / 0.35 (35118) SS BOND : bond 0.00282 / 0.15 ( 60) SS BOND : angle 0.91619 / 0.60 ( 120) hydrogen bonds : bond 0.03517 / 2.31 ( 963) hydrogen bonds : angle 6.62913 / 4.72 ( 2556) Misc. bond : bond 0.00905 / 0.45 ( 3) link_ALPHA1-2 : bond 0.00115 / 0.05 ( 6) link_ALPHA1-2 : angle 1.72141 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00185 / 0.11 ( 18) link_ALPHA1-3 : angle 1.58447 / 1.08 ( 54) link_ALPHA1-6 : bond 0.00661 / 0.36 ( 15) link_ALPHA1-6 : angle 1.67047 / 1.14 ( 45) link_BETA1-4 : bond 0.00608 / 0.40 ( 51) link_BETA1-4 : angle 1.92950 / 1.46 ( 153) link_NAG-ASN : bond 0.00850 / 0.56 ( 57) link_NAG-ASN : angle 4.11240 / 2.99 ( 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 171 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.106 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: 0.9633 (ptp) cc_final: 0.9311 (ptp) REVERT: A 150 MET cc_start: 0.8693 (mmm) cc_final: 0.8327 (mmm) REVERT: B 647 GLU cc_start: 0.9540 (pt0) cc_final: 0.9071 (tp30) REVERT: F 100 MET cc_start: 0.9557 (ptp) cc_final: 0.9125 (ptp) REVERT: F 104 MET cc_start: 0.9601 (tmm) cc_final: 0.9221 (tmm) REVERT: F 161 MET cc_start: 0.9509 (tpt) cc_final: 0.9258 (tpt) REVERT: I 626 MET cc_start: 0.9341 (ptm) cc_final: 0.7968 (ttp) REVERT: G 150 MET cc_start: 0.8829 (mmm) cc_final: 0.8344 (mmm) REVERT: G 195 ASN cc_start: 0.9569 (p0) cc_final: 0.9369 (p0) REVERT: J 530 MET cc_start: 0.8686 (ttm) cc_final: 0.8206 (ttp) REVERT: J 595 ILE cc_start: 0.9890 (tt) cc_final: 0.9066 (pt) REVERT: J 647 GLU cc_start: 0.9475 (pt0) cc_final: 0.9143 (tp30) REVERT: C 108 CYS cc_start: 0.5873 (t) cc_final: 0.4716 (t) REVERT: D 62 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9160 (mppt) REVERT: E 108 CYS cc_start: 0.5816 (t) cc_final: 0.5109 (t) REVERT: K 62 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9145 (mppt) REVERT: H 108 CYS cc_start: 0.5975 (t) cc_final: 0.5352 (t) REVERT: L 62 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9140 (mppt) REVERT: L 76 ILE cc_start: 0.8018 (mm) cc_final: 0.7783 (mt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3261 time to fit residues: 82.8544 Evaluate side-chains 147 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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: 6.9990 chunk 202 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 328 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.081654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.063418 restraints weight = 1932886.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065166 restraints weight = 458263.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066199 restraints weight = 203726.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066876 restraints weight = 133823.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067083 restraints weight = 105431.594| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1085 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25947 Z= 0.206 Angle : 0.720 13.625 35679 Z= 0.343 Chirality : 0.045 0.628 4482 Planarity : 0.005 0.112 4272 Dihedral : 5.394 31.264 3273 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 49.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.46 % Allowed : 0.76 % Favored : 98.78 % 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: -0.54 (0.15), residues: 3066 helix: -0.68 (0.24), residues: 444 sheet: -0.05 (0.15), residues: 1137 loop : -0.36 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 50 TYR 0.015 0.002 TYR C 198 PHE 0.017 0.002 PHE A 353 TRP 0.019 0.002 TRP F 35 HIS 0.006 0.002 HIS F 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (25737) covalent geometry : angle 0.65373 / 0.33 (35118) SS BOND : bond 0.00270 / 0.18 ( 60) SS BOND : angle 1.17041 / 0.80 ( 120) hydrogen bonds : bond 0.03352 / 2.20 ( 963) hydrogen bonds : angle 6.46050 / 4.60 ( 2556) Misc. bond : bond 0.00616 / 0.31 ( 3) link_ALPHA1-2 : bond 0.00092 / 0.04 ( 6) link_ALPHA1-2 : angle 1.73673 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00174 / 0.11 ( 18) link_ALPHA1-3 : angle 1.56657 / 1.07 ( 54) link_ALPHA1-6 : bond 0.00632 / 0.34 ( 15) link_ALPHA1-6 : angle 1.66870 / 1.14 ( 45) link_BETA1-4 : bond 0.00508 / 0.31 ( 51) link_BETA1-4 : angle 1.77941 / 1.31 ( 153) link_NAG-ASN : bond 0.00654 / 0.43 ( 57) link_NAG-ASN : angle 3.82891 / 2.77 ( 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 166 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.104 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 150 MET cc_start: 0.8738 (mmm) cc_final: 0.8249 (mmm) REVERT: F 104 MET cc_start: 0.9587 (tmm) cc_final: 0.9226 (tmm) REVERT: F 150 MET cc_start: 0.9388 (mtm) cc_final: 0.8838 (mtm) REVERT: F 161 MET cc_start: 0.9470 (tpt) cc_final: 0.9129 (tpt) REVERT: G 150 MET cc_start: 0.8799 (mmm) cc_final: 0.8331 (mmm) REVERT: G 195 ASN cc_start: 0.9561 (p0) cc_final: 0.9289 (p0) REVERT: J 530 MET cc_start: 0.8652 (ttm) cc_final: 0.8123 (ttp) REVERT: C 108 CYS cc_start: 0.5502 (t) cc_final: 0.4559 (t) REVERT: D 62 LYS cc_start: 0.9493 (mmmt) cc_final: 0.9181 (mppt) REVERT: E 108 CYS cc_start: 0.5647 (t) cc_final: 0.5079 (t) REVERT: K 62 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9171 (mppt) REVERT: H 108 CYS cc_start: 0.5562 (t) cc_final: 0.5025 (t) REVERT: L 62 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9189 (mppt) REVERT: L 76 ILE cc_start: 0.8009 (mm) cc_final: 0.7762 (mt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3095 time to fit residues: 76.7547 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 : 1.074 ------------------------------------------------------------------------------- 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: 8.9990 chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** L 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.081599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063235 restraints weight = 2052673.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065714 restraints weight = 452067.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.066686 restraints weight = 206886.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067339 restraints weight = 126256.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067202 restraints weight = 98215.757| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1085 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1107 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25947 Z= 0.195 Angle : 0.689 13.573 35679 Z= 0.331 Chirality : 0.044 0.549 4482 Planarity : 0.004 0.087 4272 Dihedral : 5.241 30.459 3273 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 48.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % 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: -0.46 (0.15), residues: 3066 helix: -0.48 (0.25), residues: 444 sheet: -0.06 (0.15), residues: 1101 loop : -0.30 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 50 TYR 0.016 0.001 TYR G 217 PHE 0.017 0.002 PHE A 353 TRP 0.018 0.002 TRP A 35 HIS 0.005 0.001 HIS G 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (25737) covalent geometry : angle 0.62901 / 0.32 (35118) SS BOND : bond 0.00482 / 0.19 ( 60) SS BOND : angle 1.10820 / 0.75 ( 120) hydrogen bonds : bond 0.03242 / 2.14 ( 963) hydrogen bonds : angle 6.32613 / 4.51 ( 2556) Misc. bond : bond 0.00719 / 0.36 ( 3) link_ALPHA1-2 : bond 0.00155 / 0.07 ( 6) link_ALPHA1-2 : angle 1.66104 / 0.95 ( 18) link_ALPHA1-3 : bond 0.00211 / 0.13 ( 18) link_ALPHA1-3 : angle 1.53191 / 1.04 ( 54) link_ALPHA1-6 : bond 0.00643 / 0.35 ( 15) link_ALPHA1-6 : angle 1.61919 / 1.10 ( 45) link_BETA1-4 : bond 0.00411 / 0.26 ( 51) link_BETA1-4 : angle 1.69936 / 1.26 ( 153) link_NAG-ASN : bond 0.00567 / 0.36 ( 57) link_NAG-ASN : angle 3.56519 / 2.59 ( 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 157 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.112 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 150 MET cc_start: 0.8765 (mmm) cc_final: 0.8277 (mmm) REVERT: A 161 MET cc_start: 0.9424 (tpt) cc_final: 0.9217 (tpt) REVERT: B 647 GLU cc_start: 0.9489 (pt0) cc_final: 0.9118 (tp30) REVERT: F 104 MET cc_start: 0.9581 (tmm) cc_final: 0.9218 (tmm) REVERT: F 161 MET cc_start: 0.9469 (tpt) cc_final: 0.9066 (tpt) REVERT: G 150 MET cc_start: 0.8921 (mmm) cc_final: 0.8492 (mmm) REVERT: G 161 MET cc_start: 0.9442 (tpt) cc_final: 0.9166 (tpt) REVERT: G 195 ASN cc_start: 0.9556 (p0) cc_final: 0.9243 (p0) REVERT: J 626 MET cc_start: 0.9372 (ttp) cc_final: 0.8853 (ttm) REVERT: J 647 GLU cc_start: 0.9537 (pt0) cc_final: 0.9320 (pt0) REVERT: C 108 CYS cc_start: 0.5181 (t) cc_final: 0.4342 (t) REVERT: D 62 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9216 (mppt) REVERT: E 108 CYS cc_start: 0.5269 (t) cc_final: 0.4877 (t) REVERT: K 62 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9138 (mppt) REVERT: H 108 CYS cc_start: 0.5482 (t) cc_final: 0.5183 (t) REVERT: L 62 LYS cc_start: 0.9467 (mmmt) cc_final: 0.9186 (mppt) REVERT: L 76 ILE cc_start: 0.8041 (mm) cc_final: 0.7788 (mt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3111 time to fit residues: 73.2048 Evaluate side-chains 134 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** F 425 ASN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.080586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062505 restraints weight = 1939332.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064695 restraints weight = 458918.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065641 restraints weight = 200291.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066549 restraints weight = 126534.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066409 restraints weight = 94961.028| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 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 = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1075 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25947 Z= 0.232 Angle : 0.746 13.598 35679 Z= 0.356 Chirality : 0.044 0.555 4482 Planarity : 0.005 0.086 4272 Dihedral : 5.341 30.287 3273 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 52.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.81 % Favored : 91.15 % Rotamer: Outliers : 0.46 % Allowed : 0.46 % Favored : 99.09 % 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: -0.58 (0.15), residues: 3066 helix: -0.71 (0.24), residues: 444 sheet: -0.08 (0.16), residues: 1059 loop : -0.38 (0.17), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 50 TYR 0.016 0.002 TYR C 198 PHE 0.040 0.003 PHE G 233 TRP 0.020 0.002 TRP G 69 HIS 0.005 0.002 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (25737) covalent geometry : angle 0.68795 / 0.34 (35118) SS BOND : bond 0.00234 / 0.15 ( 60) SS BOND : angle 1.10030 / 0.78 ( 120) hydrogen bonds : bond 0.03369 / 2.23 ( 963) hydrogen bonds : angle 6.47511 / 4.61 ( 2556) Misc. bond : bond 0.00613 / 0.31 ( 3) link_ALPHA1-2 : bond 0.00092 / 0.04 ( 6) link_ALPHA1-2 : angle 1.79592 / 1.03 ( 18) link_ALPHA1-3 : bond 0.00175 / 0.11 ( 18) link_ALPHA1-3 : angle 1.60315 / 1.10 ( 54) link_ALPHA1-6 : bond 0.00626 / 0.34 ( 15) link_ALPHA1-6 : angle 1.63556 / 1.10 ( 45) link_BETA1-4 : bond 0.00489 / 0.30 ( 51) link_BETA1-4 : angle 1.81387 / 1.35 ( 153) link_NAG-ASN : bond 0.00719 / 0.47 ( 57) link_NAG-ASN : angle 3.65022 / 2.61 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6702.08 seconds wall clock time: 116 minutes 18.96 seconds (6978.96 seconds total)