Starting phenix.real_space_refine on Fri Sep 19 13:40:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6edu_9038/09_2025/6edu_9038.cif Found real_map, /net/cci-nas-00/data/ceres_data/6edu_9038/09_2025/6edu_9038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2025/6edu_9038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2025/6edu_9038.map" model { file = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2025/6edu_9038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2025/6edu_9038.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 16449 2.51 5 N 4350 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26271 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "F" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 802 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 802 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "N" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "O" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 802 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "U" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "u" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "v" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" C1 NAG t 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG t 1 " occ=0.69 residue: pdb=" C1 NAG t 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG t 2 " occ=0.65 residue: pdb=" C1 BMA t 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA t 3 " occ=0.92 residue: pdb=" C1 MAN t 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN t 4 " occ=0.85 residue: pdb=" C1 MAN t 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN t 5 " occ=0.79 residue: pdb=" C1 MAN t 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN t 6 " occ=0.66 residue: pdb=" C1 NAG u 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG u 1 " occ=0.69 residue: pdb=" C1 NAG u 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG u 2 " occ=0.65 residue: pdb=" C1 BMA u 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA u 3 " occ=0.92 residue: pdb=" C1 MAN u 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN u 4 " occ=0.85 residue: pdb=" C1 MAN u 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN u 5 " occ=0.79 residue: pdb=" C1 MAN u 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN u 6 " occ=0.66 ... (remaining 6 not shown) Time building chain proxies: 6.41, per 1000 atoms: 0.24 Number of scatterers: 26271 At special positions: 0 Unit cell: (162.44, 165.06, 132.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 5331 8.00 N 4350 7.00 C 16449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.52 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS D 501 " distance=2.13 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=1.89 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.09 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.50 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.01 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.26 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.01 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.07 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.01 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 99 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 99 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 89 " 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=4, symmetry=0 Links applied ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN g 4 " - " MAN g 5 " " MAN n 4 " - " MAN n 5 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " " MAN u 4 " - " MAN u 5 " " MAN u 5 " - " MAN u 6 " " MAN v 4 " - " MAN v 5 " " MAN v 5 " - " MAN v 6 " ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " " MAN t 7 " - " MAN t 8 " " BMA u 3 " - " MAN u 4 " " MAN u 7 " - " MAN u 8 " " BMA v 3 " - " MAN v 4 " " MAN v 7 " - " MAN v 8 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA h 3 " - " MAN h 5 " " BMA o 3 " - " MAN o 5 " " BMA t 3 " - " MAN t 7 " " MAN t 7 " - " MAN t 9 " " BMA u 3 " - " MAN u 7 " " MAN u 7 " - " MAN u 9 " " BMA v 3 " - " MAN v 7 " " MAN v 7 " - " MAN v 9 " BETA1-4 " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " 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 v 2 " - " BMA v 3 " NAG-ASN " NAG A 703 " - " ASN A 616 " " NAG B 701 " - " ASN B 616 " " NAG C 701 " - " ASN C 616 " " NAG D 601 " - " ASN D 88 " " NAG D 614 " - " ASN D 295 " " NAG D 615 " - " ASN D 332 " " NAG D 616 " - " ASN D 339 " " NAG D 617 " - " ASN D 355 " " NAG D 623 " - " ASN D 392 " " NAG D 624 " - " ASN D 397 " " NAG D 627 " - " ASN D 448 " " NAG E 601 " - " ASN E 88 " " NAG E 614 " - " ASN E 295 " " NAG E 615 " - " ASN E 332 " " NAG E 616 " - " ASN E 339 " " NAG E 617 " - " ASN E 355 " " NAG E 623 " - " ASN E 392 " " NAG E 624 " - " ASN E 397 " " NAG E 627 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 614 " - " ASN F 295 " " NAG F 615 " - " ASN F 332 " " NAG F 616 " - " ASN F 339 " " NAG F 617 " - " ASN F 355 " " NAG F 623 " - " ASN F 392 " " NAG F 624 " - " ASN F 397 " " NAG F 627 " - " ASN F 448 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN C 637 " " NAG Y 1 " - " ASN D 241 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 362 " " NAG c 1 " - " ASN D 386 " " NAG d 1 " - " ASN D 413 " " NAG e 1 " - " ASN D 197 " " NAG f 1 " - " ASN E 241 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN E 276 " " NAG i 1 " - " ASN E 362 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 413 " " NAG l 1 " - " ASN E 197 " " NAG m 1 " - " ASN F 241 " " NAG n 1 " - " ASN F 262 " " NAG o 1 " - " ASN F 276 " " NAG p 1 " - " ASN F 362 " " NAG q 1 " - " ASN F 386 " " NAG r 1 " - " ASN F 413 " " NAG s 1 " - " ASN F 197 " " NAG t 1 " - " ASN F 234 " " NAG u 1 " - " ASN D 234 " " NAG v 1 " - " ASN E 234 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 64 sheets defined 14.1% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.886A pdb=" N PHE A 522 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 523' Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 565 through 595 removed outlier: 3.918A pdb=" N THR A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.083A pdb=" N TRP A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.886A pdb=" N PHE B 522 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 519 through 523' Processing helix chain 'B' and resid 529 through 544 Processing helix chain 'B' and resid 565 through 595 removed outlier: 3.918A pdb=" N THR B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.083A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 652 Processing helix chain 'C' and resid 519 through 523 removed outlier: 3.886A pdb=" N PHE C 522 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 519 through 523' Processing helix chain 'C' and resid 529 through 544 Processing helix chain 'C' and resid 565 through 595 removed outlier: 3.918A pdb=" N THR C 569 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.082A pdb=" N TRP C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 652 Processing helix chain 'D' and resid 68 through 74 removed outlier: 3.902A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.545A pdb=" N ASP D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 352 Processing helix chain 'D' and resid 368 through 372 removed outlier: 4.188A pdb=" N VAL D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 372' Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.785A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 74 removed outlier: 3.903A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 removed outlier: 3.546A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 352 Processing helix chain 'E' and resid 368 through 372 removed outlier: 4.188A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 372' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.785A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.903A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.545A pdb=" N ASP F 113 " --> pdb=" O ILE F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 Processing helix chain 'F' and resid 368 through 372 removed outlier: 4.188A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 372' Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.785A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 63 removed outlier: 4.004A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 removed outlier: 3.735A pdb=" N SER G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 63 removed outlier: 4.004A pdb=" N ASP H 63 " --> pdb=" O SER H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.734A pdb=" N SER H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 63 removed outlier: 4.004A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 removed outlier: 3.735A pdb=" N SER I 79 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 62 No H-bonds generated for 'chain 'K' and resid 60 through 62' Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'O' and resid 60 through 62 No H-bonds generated for 'chain 'O' and resid 60 through 62' Processing helix chain 'P' and resid 106 through 110 removed outlier: 3.902A pdb=" N SER P 109 " --> pdb=" O ASP P 106 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY P 110 " --> pdb=" O LYS P 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 106 through 110' Processing helix chain 'R' and resid 106 through 110 removed outlier: 3.902A pdb=" N SER R 109 " --> pdb=" O ASP R 106 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY R 110 " --> pdb=" O LYS R 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 106 through 110' Processing helix chain 'T' and resid 106 through 110 removed outlier: 3.902A pdb=" N SER T 109 " --> pdb=" O ASP T 106 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY T 110 " --> pdb=" O LYS T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 106 through 110' Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 605 removed outlier: 3.626A pdb=" N CYS B 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 603 through 605 removed outlier: 3.733A pdb=" N CYS C 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.753A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.601A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS D 239 " --> pdb=" O GLU D 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 202 Processing sheet with id=AA7, first strand: chain 'D' and resid 260 through 261 removed outlier: 6.595A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 260 through 261 removed outlier: 6.595A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN D 417 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.820A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.754A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.602A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 198 through 202 Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN E 417 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 357 through 359 removed outlier: 6.820A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.753A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.601A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS F 239 " --> pdb=" O GLU F 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 198 through 202 Processing sheet with id=AC2, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.594A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N VAL F 292 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLN F 417 " --> pdb=" O ASN F 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 359 removed outlier: 6.819A pdb=" N THR F 357 " --> pdb=" O GLU F 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC6, first strand: chain 'G' and resid 12 through 17 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'H' and resid 12 through 17 Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD1, first strand: chain 'I' and resid 12 through 17 Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.562A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL J 121 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA J 92 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL J 121 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA J 92 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.220A pdb=" N VAL K 11 " --> pdb=" O THR K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.615A pdb=" N CYS K 23 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 47 through 50 removed outlier: 6.549A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 3 through 6 removed outlier: 3.563A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP L 73 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR L 71 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.712A pdb=" N VAL L 121 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA L 92 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP L 36 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.712A pdb=" N VAL L 121 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA L 92 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.220A pdb=" N VAL M 11 " --> pdb=" O THR M 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 19 through 24 removed outlier: 3.614A pdb=" N CYS M 23 " --> pdb=" O ALA M 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 47 through 50 removed outlier: 6.549A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.563A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL N 121 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA N 92 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.713A pdb=" N VAL N 121 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA N 92 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.220A pdb=" N VAL O 11 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 19 through 24 removed outlier: 3.615A pdb=" N CYS O 23 " --> pdb=" O ALA O 73 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 47 through 50 removed outlier: 6.548A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AF3, first strand: chain 'P' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP P 53 " --> pdb=" O LYS P 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP P 37 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN P 51 " --> pdb=" O VAL P 35 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 35 " --> pdb=" O GLN P 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP P 53 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR P 33 " --> pdb=" O TRP P 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR P 101 " --> pdb=" O SER P 121 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP P 53 " --> pdb=" O LYS P 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP P 37 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN P 51 " --> pdb=" O VAL P 35 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 35 " --> pdb=" O GLN P 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP P 53 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR P 33 " --> pdb=" O TRP P 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 112 through 113 Processing sheet with id=AF6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.474A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'R' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP R 53 " --> pdb=" O LYS R 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP R 37 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN R 51 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL R 35 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP R 53 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR R 33 " --> pdb=" O TRP R 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR R 101 " --> pdb=" O SER R 121 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP R 53 " --> pdb=" O LYS R 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP R 37 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN R 51 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL R 35 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP R 53 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR R 33 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 112 through 113 Processing sheet with id=AG3, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.474A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'T' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP T 53 " --> pdb=" O LYS T 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP T 37 " --> pdb=" O ILE T 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN T 51 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL T 35 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP T 53 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR T 33 " --> pdb=" O TRP T 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR T 101 " --> pdb=" O SER T 121 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 56 through 59 removed outlier: 4.102A pdb=" N TRP T 53 " --> pdb=" O LYS T 56 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP T 37 " --> pdb=" O ILE T 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN T 51 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL T 35 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP T 53 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N TYR T 33 " --> pdb=" O TRP T 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 112 through 113 Processing sheet with id=AG9, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AH1, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.474A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR U 50 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL U 34 " --> pdb=" O TYR U 50 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2226 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: 6.26 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8010 1.34 - 1.47: 6866 1.47 - 1.59: 11722 1.59 - 1.72: 3 1.72 - 1.84: 189 Bond restraints: 26790 Sorted by residual: bond pdb=" C ALA E 204 " pdb=" N CYS E 205 " ideal model delta sigma weight residual 1.332 1.540 -0.208 1.14e-02 7.69e+03 3.33e+02 bond pdb=" C ALA F 204 " pdb=" N CYS F 205 " ideal model delta sigma weight residual 1.332 1.273 0.058 8.60e-03 1.35e+04 4.61e+01 bond pdb=" N THR F 163 " pdb=" CA THR F 163 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.48e+01 bond pdb=" N THR D 163 " pdb=" CA THR D 163 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" N THR E 163 " pdb=" CA THR E 163 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 ... (remaining 26785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.21: 36305 7.21 - 14.41: 113 14.41 - 21.62: 4 21.62 - 28.83: 2 28.83 - 36.03: 5 Bond angle restraints: 36429 Sorted by residual: angle pdb=" O ALA F 204 " pdb=" C ALA F 204 " pdb=" N CYS F 205 " ideal model delta sigma weight residual 122.65 157.71 -35.06 1.22e+00 6.72e-01 8.26e+02 angle pdb=" C ALA F 204 " pdb=" N CYS F 205 " pdb=" CA CYS F 205 " ideal model delta sigma weight residual 122.00 90.97 31.03 1.08e+00 8.57e-01 8.26e+02 angle pdb=" CA ALA F 204 " pdb=" C ALA F 204 " pdb=" N CYS F 205 " ideal model delta sigma weight residual 115.29 79.26 36.03 1.44e+00 4.82e-01 6.26e+02 angle pdb=" O ALA E 204 " pdb=" C ALA E 204 " pdb=" N CYS E 205 " ideal model delta sigma weight residual 122.65 152.88 -30.23 1.22e+00 6.72e-01 6.14e+02 angle pdb=" CA ALA E 204 " pdb=" C ALA E 204 " pdb=" N CYS E 205 " ideal model delta sigma weight residual 115.29 85.42 29.87 1.44e+00 4.82e-01 4.30e+02 ... (remaining 36424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 16390 21.53 - 43.06: 747 43.06 - 64.60: 156 64.60 - 86.13: 82 86.13 - 107.66: 49 Dihedral angle restraints: 17424 sinusoidal: 8154 harmonic: 9270 Sorted by residual: dihedral pdb=" C THR D 163 " pdb=" N THR D 163 " pdb=" CA THR D 163 " pdb=" CB THR D 163 " ideal model delta harmonic sigma weight residual -122.00 -150.22 28.22 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" C THR E 163 " pdb=" N THR E 163 " pdb=" CA THR E 163 " pdb=" CB THR E 163 " ideal model delta harmonic sigma weight residual -122.00 -150.18 28.18 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" C THR F 163 " pdb=" N THR F 163 " pdb=" CA THR F 163 " pdb=" CB THR F 163 " ideal model delta harmonic sigma weight residual -122.00 -150.11 28.11 0 2.50e+00 1.60e-01 1.26e+02 ... (remaining 17421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 4416 0.209 - 0.418: 75 0.418 - 0.627: 6 0.627 - 0.836: 3 0.836 - 1.044: 3 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.12e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.23e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.08e+02 ... (remaining 4500 not shown) Planarity restraints: 4512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 2 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG l 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG l 2 " -0.141 2.00e-02 2.50e+03 pdb=" N2 NAG l 2 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG l 2 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 1 " -0.332 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG l 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG l 1 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG l 1 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG l 1 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG s 2 " 0.140 2.00e-02 2.50e+03 1.16e-01 1.68e+02 pdb=" C7 NAG s 2 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG s 2 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG s 2 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG s 2 " -0.019 2.00e-02 2.50e+03 ... (remaining 4509 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 66 2.41 - 3.03: 14853 3.03 - 3.65: 36924 3.65 - 4.28: 56179 4.28 - 4.90: 91658 Nonbonded interactions: 199680 Sorted by model distance: nonbonded pdb=" OH TYR J 103 " pdb=" OD2 ASP K 52 " model vdw 1.783 3.040 nonbonded pdb=" O SER F 158 " pdb=" OG SER F 158 " model vdw 1.976 3.040 nonbonded pdb=" O3 NAG e 2 " pdb=" O7 NAG e 2 " model vdw 2.056 3.040 nonbonded pdb=" O3 NAG s 2 " pdb=" O7 NAG s 2 " model vdw 2.103 3.040 nonbonded pdb=" CG2 THR F 198 " pdb=" O ASN J 104 " model vdw 2.131 3.460 ... (remaining 199675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'g' selection = chain 'h' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'b' selection = chain 'i' selection = chain 'p' } ncs_group { reference = chain 't' selection = chain 'u' selection = chain 'v' } 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.730 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.009 0.491 26962 Z= 0.489 Angle : 1.453 36.033 36888 Z= 0.794 Chirality : 0.082 1.044 4503 Planarity : 0.018 0.446 4458 Dihedral : 14.778 107.660 11343 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.13 % Favored : 87.06 % Rotamer: Outliers : 2.62 % Allowed : 5.12 % Favored : 92.26 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 4.55 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.56 (0.12), residues: 3183 helix: -2.59 (0.21), residues: 399 sheet: -2.26 (0.14), residues: 1014 loop : -3.75 (0.11), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 38 TYR 0.034 0.003 TYR U 92 PHE 0.030 0.003 PHE E 353 TRP 0.070 0.004 TRP F 45 HIS 0.015 0.002 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00754 (26790) covalent geometry : angle 1.37278 (36429) SS BOND : bond 0.11121 ( 45) SS BOND : angle 5.01082 ( 90) hydrogen bonds : bond 0.17380 ( 779) hydrogen bonds : angle 9.28671 ( 2226) Misc. bond : bond 0.09519 ( 4) link_ALPHA1-2 : bond 0.00381 ( 9) link_ALPHA1-2 : angle 1.94706 ( 27) link_ALPHA1-3 : bond 0.00431 ( 12) link_ALPHA1-3 : angle 1.78128 ( 36) link_ALPHA1-6 : bond 0.00083 ( 9) link_ALPHA1-6 : angle 1.64353 ( 27) link_BETA1-4 : bond 0.01490 ( 39) link_BETA1-4 : angle 3.82396 ( 117) link_NAG-ASN : bond 0.01405 ( 54) link_NAG-ASN : angle 5.52766 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 872 time to evaluate : 0.952 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: A 629 MET cc_start: 0.6135 (mmt) cc_final: 0.5491 (mmp) REVERT: B 529 THR cc_start: 0.8325 (p) cc_final: 0.8085 (t) REVERT: B 530 MET cc_start: 0.7175 (mtp) cc_final: 0.6905 (mtp) REVERT: B 570 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8389 (p) REVERT: B 620 ASN cc_start: 0.7970 (t0) cc_final: 0.7646 (p0) REVERT: C 589 ASP cc_start: 0.9034 (m-30) cc_final: 0.8784 (m-30) REVERT: C 620 ASN cc_start: 0.7869 (t0) cc_final: 0.7508 (p0) REVERT: D 95 MET cc_start: 0.6817 (ttp) cc_final: 0.6529 (mtp) REVERT: D 107 ASP cc_start: 0.8209 (t70) cc_final: 0.7856 (t70) REVERT: D 166 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.4994 (ptm160) REVERT: D 423 ILE cc_start: 0.8604 (mt) cc_final: 0.7990 (mt) REVERT: D 475 MET cc_start: 0.7147 (mmt) cc_final: 0.6636 (tpp) REVERT: E 95 MET cc_start: 0.6901 (ttp) cc_final: 0.6685 (mtp) REVERT: E 194 ILE cc_start: 0.7688 (mp) cc_final: 0.6682 (mm) REVERT: E 353 PHE cc_start: 0.7835 (m-10) cc_final: 0.7504 (m-80) REVERT: E 475 MET cc_start: 0.7584 (mmt) cc_final: 0.7147 (mmm) REVERT: F 44 VAL cc_start: 0.8645 (t) cc_final: 0.7775 (t) REVERT: F 327 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6593 (mtm180) REVERT: F 413 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.5493 (t0) REVERT: F 423 ILE cc_start: 0.8296 (mt) cc_final: 0.7683 (tt) REVERT: F 435 TYR cc_start: 0.5011 (m-80) cc_final: 0.4637 (m-10) REVERT: G 5 LEU cc_start: 0.8176 (mp) cc_final: 0.7907 (tt) REVERT: G 13 GLU cc_start: 0.7574 (tp30) cc_final: 0.7104 (tm-30) REVERT: H 5 LEU cc_start: 0.8023 (mp) cc_final: 0.7556 (tt) REVERT: H 79 SER cc_start: 0.8449 (m) cc_final: 0.7609 (p) REVERT: I 5 LEU cc_start: 0.7905 (mp) cc_final: 0.7591 (tt) REVERT: I 79 SER cc_start: 0.8525 (m) cc_final: 0.7938 (p) REVERT: J 72 GLU cc_start: 0.7286 (tt0) cc_final: 0.6914 (tt0) REVERT: J 81 MET cc_start: 0.7666 (tmm) cc_final: 0.7422 (tmm) REVERT: J 95 TYR cc_start: 0.7907 (m-80) cc_final: 0.7247 (m-80) REVERT: K 50 ILE cc_start: 0.6959 (mt) cc_final: 0.6190 (mm) REVERT: L 33 SER cc_start: 0.5840 (m) cc_final: 0.5382 (t) REVERT: L 76 THR cc_start: 0.8018 (p) cc_final: 0.7146 (p) REVERT: L 81 MET cc_start: 0.7761 (tmm) cc_final: 0.7396 (tmm) REVERT: L 88 SER cc_start: 0.6997 (m) cc_final: 0.6589 (t) REVERT: M 50 ILE cc_start: 0.6989 (mt) cc_final: 0.6259 (mm) REVERT: M 51 PHE cc_start: 0.7169 (p90) cc_final: 0.6840 (p90) REVERT: N 33 SER cc_start: 0.6182 (m) cc_final: 0.5490 (t) REVERT: N 55 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7531 (mm-30) REVERT: N 67 ARG cc_start: 0.3838 (ptt180) cc_final: 0.3230 (ptt-90) REVERT: N 76 THR cc_start: 0.8059 (p) cc_final: 0.7680 (p) REVERT: N 88 SER cc_start: 0.6534 (m) cc_final: 0.5969 (t) REVERT: N 90 ASP cc_start: 0.5509 (m-30) cc_final: 0.5243 (m-30) REVERT: N 95 TYR cc_start: 0.7772 (m-80) cc_final: 0.7484 (m-80) REVERT: O 49 LEU cc_start: 0.6222 (tp) cc_final: 0.6016 (tp) REVERT: O 93 TRP cc_start: 0.7789 (t-100) cc_final: 0.7584 (t-100) REVERT: P 111 LEU cc_start: 0.8619 (mm) cc_final: 0.8243 (mt) REVERT: P 122 TRP cc_start: 0.8704 (m100) cc_final: 0.8498 (m100) REVERT: Q 33 TRP cc_start: 0.8872 (m100) cc_final: 0.7871 (m100) REVERT: Q 78 ASN cc_start: 0.8822 (t0) cc_final: 0.8428 (t0) REVERT: R 90 THR cc_start: 0.8559 (p) cc_final: 0.8256 (p) REVERT: R 105 TYR cc_start: 0.8199 (t80) cc_final: 0.7834 (t80) REVERT: R 111 LEU cc_start: 0.8927 (mm) cc_final: 0.8398 (mt) REVERT: S 2 ILE cc_start: 0.8918 (mt) cc_final: 0.8258 (pt) REVERT: S 78 ASN cc_start: 0.8171 (t0) cc_final: 0.7211 (t0) REVERT: T 63 PHE cc_start: 0.7810 (t80) cc_final: 0.7514 (t80) REVERT: T 67 VAL cc_start: 0.8624 (t) cc_final: 0.8090 (m) REVERT: T 105 TYR cc_start: 0.8214 (t80) cc_final: 0.7946 (t80) REVERT: T 111 LEU cc_start: 0.8925 (mm) cc_final: 0.8363 (mt) REVERT: T 122 TRP cc_start: 0.8700 (m100) cc_final: 0.8097 (m100) REVERT: U 2 ILE cc_start: 0.8741 (mt) cc_final: 0.8128 (pt) REVERT: U 33 TRP cc_start: 0.9140 (m100) cc_final: 0.8860 (m100) REVERT: U 70 THR cc_start: 0.7227 (p) cc_final: 0.6906 (p) REVERT: U 78 ASN cc_start: 0.8513 (t0) cc_final: 0.7540 (t0) outliers start: 69 outliers final: 18 residues processed: 910 average time/residue: 0.1834 time to fit residues: 258.2337 Evaluate side-chains 489 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 468 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN A 641 HIS B 630 GLN B 641 HIS C 630 GLN C 641 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN I 73 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 104 ASN K 40 GLN L 35 HIS M 7 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.131135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.109903 restraints weight = 54506.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.111194 restraints weight = 47035.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.112414 restraints weight = 38993.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112768 restraints weight = 31661.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.112968 restraints weight = 29507.421| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26962 Z= 0.280 Angle : 1.034 13.958 36888 Z= 0.500 Chirality : 0.056 0.453 4503 Planarity : 0.008 0.145 4458 Dihedral : 13.280 81.292 5931 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.00 % Favored : 87.46 % Rotamer: Outliers : 0.19 % Allowed : 3.94 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.16 (0.13), residues: 3183 helix: -1.42 (0.24), residues: 387 sheet: -2.10 (0.15), residues: 1068 loop : -3.65 (0.11), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 273 TYR 0.029 0.003 TYR L 103 PHE 0.032 0.003 PHE P 63 TRP 0.039 0.003 TRP F 45 HIS 0.009 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00618 (26790) covalent geometry : angle 0.96764 (36429) SS BOND : bond 0.00978 ( 45) SS BOND : angle 1.91713 ( 90) hydrogen bonds : bond 0.04887 ( 779) hydrogen bonds : angle 7.17580 ( 2226) Misc. bond : bond 0.00184 ( 4) link_ALPHA1-2 : bond 0.00500 ( 9) link_ALPHA1-2 : angle 1.81021 ( 27) link_ALPHA1-3 : bond 0.00854 ( 12) link_ALPHA1-3 : angle 2.89148 ( 36) link_ALPHA1-6 : bond 0.00305 ( 9) link_ALPHA1-6 : angle 2.11786 ( 27) link_BETA1-4 : bond 0.01070 ( 39) link_BETA1-4 : angle 2.75669 ( 117) link_NAG-ASN : bond 0.00899 ( 54) link_NAG-ASN : angle 4.69332 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 594 time to evaluate : 0.981 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: A 629 MET cc_start: 0.7237 (mmt) cc_final: 0.6904 (mmp) REVERT: B 530 MET cc_start: 0.7357 (mtp) cc_final: 0.6809 (mtp) REVERT: B 620 ASN cc_start: 0.7790 (t0) cc_final: 0.7549 (p0) REVERT: B 629 MET cc_start: 0.7152 (mmt) cc_final: 0.6294 (mmp) REVERT: C 565 MET cc_start: 0.5444 (mmm) cc_final: 0.5235 (mmp) REVERT: C 589 ASP cc_start: 0.9125 (m-30) cc_final: 0.8569 (m-30) REVERT: C 629 MET cc_start: 0.7043 (mmt) cc_final: 0.6320 (mmp) REVERT: D 40 TYR cc_start: 0.8598 (t80) cc_final: 0.8122 (t80) REVERT: D 95 MET cc_start: 0.7550 (ttp) cc_final: 0.6915 (ttp) REVERT: D 423 ILE cc_start: 0.8481 (mt) cc_final: 0.7844 (mt) REVERT: D 477 ASP cc_start: 0.7290 (t0) cc_final: 0.7075 (t0) REVERT: E 95 MET cc_start: 0.7759 (ttp) cc_final: 0.6822 (ttp) REVERT: E 160 ASN cc_start: 0.7929 (p0) cc_final: 0.7599 (p0) REVERT: E 353 PHE cc_start: 0.7778 (m-10) cc_final: 0.7555 (m-80) REVERT: E 426 MET cc_start: 0.8388 (mtp) cc_final: 0.8116 (mtp) REVERT: E 475 MET cc_start: 0.7668 (mmt) cc_final: 0.7374 (tpp) REVERT: E 477 ASP cc_start: 0.7603 (t70) cc_final: 0.7261 (t0) REVERT: F 40 TYR cc_start: 0.8606 (t80) cc_final: 0.8368 (t80) REVERT: F 475 MET cc_start: 0.8643 (mmp) cc_final: 0.7803 (mmm) REVERT: G 5 LEU cc_start: 0.8227 (mp) cc_final: 0.7869 (tt) REVERT: G 16 CYS cc_start: 0.4312 (m) cc_final: 0.3571 (m) REVERT: H 5 LEU cc_start: 0.7865 (mp) cc_final: 0.7259 (tt) REVERT: H 78 ASP cc_start: 0.8241 (m-30) cc_final: 0.7947 (m-30) REVERT: H 79 SER cc_start: 0.8408 (m) cc_final: 0.7656 (p) REVERT: I 5 LEU cc_start: 0.7787 (mp) cc_final: 0.7394 (tt) REVERT: I 58 ARG cc_start: 0.7625 (ptm-80) cc_final: 0.7375 (ptm-80) REVERT: I 79 SER cc_start: 0.8484 (m) cc_final: 0.7897 (p) REVERT: J 10 GLU cc_start: 0.7310 (tp30) cc_final: 0.6281 (tp30) REVERT: J 76 THR cc_start: 0.8171 (p) cc_final: 0.7888 (p) REVERT: J 81 MET cc_start: 0.7921 (tmm) cc_final: 0.7622 (tmm) REVERT: J 95 TYR cc_start: 0.7744 (m-80) cc_final: 0.7359 (m-80) REVERT: L 12 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7928 (mmt180) REVERT: L 55 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6846 (mm-30) REVERT: L 76 THR cc_start: 0.7926 (p) cc_final: 0.7354 (p) REVERT: L 78 THR cc_start: 0.7740 (p) cc_final: 0.6773 (p) REVERT: L 88 SER cc_start: 0.6742 (m) cc_final: 0.6370 (t) REVERT: L 112 LEU cc_start: 0.8452 (mt) cc_final: 0.8192 (mp) REVERT: N 95 TYR cc_start: 0.7544 (m-80) cc_final: 0.7284 (m-80) REVERT: O 93 TRP cc_start: 0.8082 (t-100) cc_final: 0.7717 (t-100) REVERT: Q 2 ILE cc_start: 0.8887 (mt) cc_final: 0.8634 (mm) REVERT: Q 78 ASN cc_start: 0.8866 (t0) cc_final: 0.7681 (t0) REVERT: R 105 TYR cc_start: 0.8283 (t80) cc_final: 0.7890 (t80) REVERT: S 9 SER cc_start: 0.7533 (m) cc_final: 0.7239 (t) REVERT: S 78 ASN cc_start: 0.8358 (t0) cc_final: 0.7266 (t0) REVERT: S 101 GLN cc_start: 0.7289 (mt0) cc_final: 0.6915 (mp10) REVERT: T 105 TYR cc_start: 0.8327 (t80) cc_final: 0.7926 (t80) REVERT: U 78 ASN cc_start: 0.8571 (t0) cc_final: 0.7463 (t0) REVERT: U 101 GLN cc_start: 0.7060 (mt0) cc_final: 0.6799 (mp10) outliers start: 5 outliers final: 0 residues processed: 598 average time/residue: 0.1698 time to fit residues: 161.6268 Evaluate side-chains 401 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 65 optimal weight: 0.5980 chunk 284 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 239 optimal weight: 0.2980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN I 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN M 33 ASN M 40 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN O 40 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN U 91 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.124850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.100745 restraints weight = 50322.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102326 restraints weight = 31567.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103369 restraints weight = 24842.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104215 restraints weight = 21010.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104582 restraints weight = 18493.129| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26962 Z= 0.185 Angle : 0.890 13.728 36888 Z= 0.436 Chirality : 0.052 0.364 4503 Planarity : 0.006 0.123 4458 Dihedral : 11.693 68.543 5931 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.56 % Favored : 89.00 % Rotamer: Outliers : 0.23 % Allowed : 3.41 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.84 (0.13), residues: 3183 helix: -1.09 (0.25), residues: 384 sheet: -1.68 (0.15), residues: 1005 loop : -3.57 (0.11), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 273 TYR 0.026 0.002 TYR D 217 PHE 0.035 0.002 PHE T 63 TRP 0.030 0.002 TRP F 479 HIS 0.005 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00411 (26790) covalent geometry : angle 0.82931 (36429) SS BOND : bond 0.00600 ( 45) SS BOND : angle 1.83366 ( 90) hydrogen bonds : bond 0.04234 ( 779) hydrogen bonds : angle 6.66309 ( 2226) Misc. bond : bond 0.00116 ( 4) link_ALPHA1-2 : bond 0.00339 ( 9) link_ALPHA1-2 : angle 1.68803 ( 27) link_ALPHA1-3 : bond 0.01070 ( 12) link_ALPHA1-3 : angle 1.86773 ( 36) link_ALPHA1-6 : bond 0.00439 ( 9) link_ALPHA1-6 : angle 1.87244 ( 27) link_BETA1-4 : bond 0.01025 ( 39) link_BETA1-4 : angle 2.54266 ( 117) link_NAG-ASN : bond 0.00875 ( 54) link_NAG-ASN : angle 4.16795 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 586 time to evaluate : 0.985 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: A 591 GLN cc_start: 0.8542 (pm20) cc_final: 0.8157 (pm20) REVERT: A 629 MET cc_start: 0.7104 (mmt) cc_final: 0.6895 (mmp) REVERT: A 643 TYR cc_start: 0.7994 (m-80) cc_final: 0.7692 (m-80) REVERT: B 589 ASP cc_start: 0.8872 (m-30) cc_final: 0.7855 (m-30) REVERT: B 620 ASN cc_start: 0.7922 (t0) cc_final: 0.7556 (p0) REVERT: B 629 MET cc_start: 0.7416 (mmt) cc_final: 0.6400 (mmp) REVERT: B 631 TRP cc_start: 0.5885 (m-90) cc_final: 0.4679 (m-10) REVERT: C 589 ASP cc_start: 0.9194 (m-30) cc_final: 0.8453 (m-30) REVERT: C 620 ASN cc_start: 0.7796 (t0) cc_final: 0.7385 (p0) REVERT: C 629 MET cc_start: 0.6864 (mmt) cc_final: 0.6280 (mmp) REVERT: D 95 MET cc_start: 0.7864 (ttp) cc_final: 0.7072 (ttp) REVERT: D 104 MET cc_start: 0.8569 (tpp) cc_final: 0.8057 (tpp) REVERT: D 423 ILE cc_start: 0.8543 (mt) cc_final: 0.7954 (mt) REVERT: D 477 ASP cc_start: 0.7451 (t0) cc_final: 0.7227 (t0) REVERT: E 95 MET cc_start: 0.7897 (ttp) cc_final: 0.6998 (ttp) REVERT: E 160 ASN cc_start: 0.8080 (p0) cc_final: 0.7712 (p0) REVERT: E 477 ASP cc_start: 0.7650 (t70) cc_final: 0.7402 (t0) REVERT: F 327 ARG cc_start: 0.6871 (mtt90) cc_final: 0.6407 (mtm180) REVERT: F 423 ILE cc_start: 0.8886 (mt) cc_final: 0.8578 (mt) REVERT: F 475 MET cc_start: 0.8705 (mmp) cc_final: 0.8189 (mmm) REVERT: G 5 LEU cc_start: 0.8211 (mp) cc_final: 0.7906 (tt) REVERT: G 96 LEU cc_start: 0.7801 (mt) cc_final: 0.7552 (mt) REVERT: H 5 LEU cc_start: 0.7837 (mp) cc_final: 0.7383 (tt) REVERT: H 78 ASP cc_start: 0.8128 (m-30) cc_final: 0.7841 (m-30) REVERT: H 79 SER cc_start: 0.8398 (m) cc_final: 0.7636 (p) REVERT: I 5 LEU cc_start: 0.7782 (mp) cc_final: 0.7400 (tt) REVERT: I 79 SER cc_start: 0.8329 (m) cc_final: 0.7864 (p) REVERT: J 10 GLU cc_start: 0.7622 (tp30) cc_final: 0.7091 (tp30) REVERT: J 46 GLU cc_start: 0.8977 (tp30) cc_final: 0.8774 (tp30) REVERT: J 95 TYR cc_start: 0.7900 (m-80) cc_final: 0.7502 (m-80) REVERT: J 107 THR cc_start: 0.6334 (m) cc_final: 0.5815 (m) REVERT: K 109 LEU cc_start: 0.8160 (tp) cc_final: 0.7954 (tp) REVERT: L 55 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6575 (mm-30) REVERT: L 80 TYR cc_start: 0.6790 (m-80) cc_final: 0.6565 (m-10) REVERT: L 107 THR cc_start: 0.6701 (m) cc_final: 0.6478 (m) REVERT: M 32 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8194 (ttpt) REVERT: M 77 ILE cc_start: 0.6929 (tp) cc_final: 0.6695 (mp) REVERT: M 93 TRP cc_start: 0.7997 (t-100) cc_final: 0.7310 (t60) REVERT: M 101 GLN cc_start: 0.8788 (tt0) cc_final: 0.8382 (tt0) REVERT: N 10 GLU cc_start: 0.7307 (tp30) cc_final: 0.6637 (tm-30) REVERT: N 46 GLU cc_start: 0.9001 (tp30) cc_final: 0.8633 (tp30) REVERT: N 78 THR cc_start: 0.7844 (p) cc_final: 0.7287 (p) REVERT: N 95 TYR cc_start: 0.7729 (m-80) cc_final: 0.7402 (m-80) REVERT: O 32 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7888 (ttpp) REVERT: O 34 TYR cc_start: 0.7343 (m-80) cc_final: 0.7134 (m-80) REVERT: O 99 THR cc_start: 0.7966 (p) cc_final: 0.7442 (p) REVERT: Q 23 CYS cc_start: 0.4104 (p) cc_final: 0.3860 (p) REVERT: Q 70 THR cc_start: 0.7211 (p) cc_final: 0.6669 (p) REVERT: Q 78 ASN cc_start: 0.8818 (t0) cc_final: 0.7804 (t0) REVERT: R 1 GLN cc_start: 0.7751 (pm20) cc_final: 0.7014 (pm20) REVERT: S 9 SER cc_start: 0.7542 (m) cc_final: 0.7244 (t) REVERT: S 78 ASN cc_start: 0.8497 (t0) cc_final: 0.7379 (t0) REVERT: T 111 LEU cc_start: 0.9190 (mm) cc_final: 0.8745 (mt) REVERT: T 121 SER cc_start: 0.8950 (t) cc_final: 0.8732 (t) REVERT: T 122 TRP cc_start: 0.8838 (m100) cc_final: 0.7897 (m100) REVERT: T 124 GLN cc_start: 0.7368 (pp30) cc_final: 0.7103 (pp30) REVERT: U 23 CYS cc_start: 0.3013 (p) cc_final: 0.2145 (p) REVERT: U 36 TRP cc_start: 0.6825 (m100) cc_final: 0.6567 (m100) REVERT: U 78 ASN cc_start: 0.8595 (t0) cc_final: 0.7580 (t0) outliers start: 6 outliers final: 0 residues processed: 592 average time/residue: 0.1551 time to fit residues: 149.0053 Evaluate side-chains 421 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 37 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 293 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN I 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS K 7 GLN K 33 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS N 101 ASN O 7 GLN P 36 ASN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 HIS R 51 GLN S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 HIS U 32 ASN ** U 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.100628 restraints weight = 49945.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103146 restraints weight = 33025.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104422 restraints weight = 22673.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104927 restraints weight = 17908.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105423 restraints weight = 16913.520| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26962 Z= 0.174 Angle : 0.861 13.701 36888 Z= 0.420 Chirality : 0.051 0.353 4503 Planarity : 0.006 0.111 4458 Dihedral : 10.403 64.243 5931 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.34 % Favored : 88.19 % Rotamer: Outliers : 0.27 % Allowed : 4.06 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.13), residues: 3183 helix: -0.90 (0.26), residues: 387 sheet: -1.50 (0.15), residues: 1005 loop : -3.46 (0.11), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 273 TYR 0.021 0.002 TYR D 484 PHE 0.032 0.002 PHE T 63 TRP 0.031 0.002 TRP C 631 HIS 0.006 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00386 (26790) covalent geometry : angle 0.80513 (36429) SS BOND : bond 0.00538 ( 45) SS BOND : angle 1.74933 ( 90) hydrogen bonds : bond 0.03904 ( 779) hydrogen bonds : angle 6.28513 ( 2226) Misc. bond : bond 0.00050 ( 4) link_ALPHA1-2 : bond 0.00289 ( 9) link_ALPHA1-2 : angle 1.66495 ( 27) link_ALPHA1-3 : bond 0.01028 ( 12) link_ALPHA1-3 : angle 1.88183 ( 36) link_ALPHA1-6 : bond 0.00561 ( 9) link_ALPHA1-6 : angle 1.76949 ( 27) link_BETA1-4 : bond 0.00947 ( 39) link_BETA1-4 : angle 2.39527 ( 117) link_NAG-ASN : bond 0.00763 ( 54) link_NAG-ASN : angle 3.91213 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 561 time to evaluate : 0.927 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: B 589 ASP cc_start: 0.8893 (m-30) cc_final: 0.8652 (m-30) REVERT: B 620 ASN cc_start: 0.7905 (t0) cc_final: 0.7568 (p0) REVERT: B 629 MET cc_start: 0.7360 (mmt) cc_final: 0.6794 (mmp) REVERT: C 589 ASP cc_start: 0.9130 (m-30) cc_final: 0.8441 (m-30) REVERT: C 620 ASN cc_start: 0.7803 (t0) cc_final: 0.7426 (p0) REVERT: C 629 MET cc_start: 0.7173 (mmt) cc_final: 0.6705 (mmp) REVERT: D 95 MET cc_start: 0.7795 (ttp) cc_final: 0.7033 (ttp) REVERT: D 104 MET cc_start: 0.8564 (tpp) cc_final: 0.8116 (tpp) REVERT: D 423 ILE cc_start: 0.8551 (mt) cc_final: 0.8002 (mt) REVERT: D 463 ASN cc_start: 0.8021 (p0) cc_final: 0.7761 (p0) REVERT: E 95 MET cc_start: 0.7919 (ttp) cc_final: 0.6979 (ttp) REVERT: E 160 ASN cc_start: 0.8037 (p0) cc_final: 0.7780 (p0) REVERT: E 475 MET cc_start: 0.7859 (mmp) cc_final: 0.7125 (tpp) REVERT: E 477 ASP cc_start: 0.7802 (t70) cc_final: 0.7524 (t0) REVERT: E 479 TRP cc_start: 0.6549 (m-90) cc_final: 0.6273 (m-90) REVERT: F 423 ILE cc_start: 0.8851 (mt) cc_final: 0.8569 (mt) REVERT: G 5 LEU cc_start: 0.8010 (mp) cc_final: 0.7752 (tt) REVERT: G 96 LEU cc_start: 0.7704 (mt) cc_final: 0.7437 (mt) REVERT: H 5 LEU cc_start: 0.7815 (mp) cc_final: 0.7376 (tt) REVERT: H 78 ASP cc_start: 0.8106 (m-30) cc_final: 0.7856 (m-30) REVERT: H 79 SER cc_start: 0.8405 (m) cc_final: 0.7625 (p) REVERT: I 5 LEU cc_start: 0.7770 (mp) cc_final: 0.7415 (tt) REVERT: I 79 SER cc_start: 0.8321 (m) cc_final: 0.7818 (p) REVERT: J 46 GLU cc_start: 0.8882 (tp30) cc_final: 0.8648 (tp30) REVERT: J 81 MET cc_start: 0.7890 (tmm) cc_final: 0.7629 (tmm) REVERT: J 95 TYR cc_start: 0.7751 (m-80) cc_final: 0.7445 (m-80) REVERT: L 55 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6649 (mm-30) REVERT: L 78 THR cc_start: 0.7677 (p) cc_final: 0.7322 (p) REVERT: L 87 ARG cc_start: 0.8417 (mmt90) cc_final: 0.8214 (mmt90) REVERT: L 88 SER cc_start: 0.6471 (m) cc_final: 0.6077 (t) REVERT: L 107 THR cc_start: 0.6625 (m) cc_final: 0.6408 (m) REVERT: M 93 TRP cc_start: 0.7928 (t-100) cc_final: 0.7425 (t60) REVERT: M 101 GLN cc_start: 0.8578 (tt0) cc_final: 0.8139 (tt0) REVERT: N 46 GLU cc_start: 0.8861 (tp30) cc_final: 0.8568 (tp30) REVERT: N 78 THR cc_start: 0.7892 (p) cc_final: 0.7363 (p) REVERT: N 95 TYR cc_start: 0.7671 (m-80) cc_final: 0.7443 (m-80) REVERT: N 112 LEU cc_start: 0.8444 (mt) cc_final: 0.7886 (mp) REVERT: O 32 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7981 (ttpp) REVERT: O 50 ILE cc_start: 0.7018 (mt) cc_final: 0.6814 (mt) REVERT: Q 2 ILE cc_start: 0.9306 (mm) cc_final: 0.9079 (mm) REVERT: Q 70 THR cc_start: 0.7314 (p) cc_final: 0.6961 (p) REVERT: Q 78 ASN cc_start: 0.8740 (t0) cc_final: 0.7675 (t0) REVERT: R 51 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: R 122 TRP cc_start: 0.8474 (m100) cc_final: 0.8050 (m-10) REVERT: R 124 GLN cc_start: 0.7399 (pp30) cc_final: 0.7122 (tm-30) REVERT: S 9 SER cc_start: 0.7491 (m) cc_final: 0.7278 (t) REVERT: S 24 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6875 (mtp85) REVERT: S 78 ASN cc_start: 0.8485 (t0) cc_final: 0.7339 (t0) REVERT: T 111 LEU cc_start: 0.9168 (mm) cc_final: 0.8665 (mt) REVERT: T 122 TRP cc_start: 0.8825 (m100) cc_final: 0.7839 (m100) REVERT: T 124 GLN cc_start: 0.7564 (pp30) cc_final: 0.7221 (tm-30) REVERT: U 23 CYS cc_start: 0.2506 (p) cc_final: 0.2050 (p) REVERT: U 36 TRP cc_start: 0.7049 (m100) cc_final: 0.6619 (m100) REVERT: U 66 SER cc_start: 0.8800 (t) cc_final: 0.8288 (m) REVERT: U 70 THR cc_start: 0.7314 (p) cc_final: 0.6752 (p) REVERT: U 78 ASN cc_start: 0.8523 (t0) cc_final: 0.8107 (t0) outliers start: 7 outliers final: 2 residues processed: 568 average time/residue: 0.1572 time to fit residues: 145.4914 Evaluate side-chains 425 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 422 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 127 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 236 optimal weight: 0.0870 chunk 2 optimal weight: 0.0270 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN F 99 ASN G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 101 ASN M 7 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN N 104 ASN O 7 GLN P 3 HIS Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 HIS R 124 GLN S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN T 124 GLN U 101 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.129068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104541 restraints weight = 48958.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.107255 restraints weight = 29688.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.108477 restraints weight = 21136.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.109789 restraints weight = 17439.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.109966 restraints weight = 15636.611| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26962 Z= 0.141 Angle : 0.824 13.678 36888 Z= 0.403 Chirality : 0.051 0.355 4503 Planarity : 0.005 0.086 4458 Dihedral : 9.318 60.136 5931 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.55 % Favored : 90.07 % Rotamer: Outliers : 0.23 % Allowed : 1.74 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.13), residues: 3183 helix: -0.57 (0.26), residues: 387 sheet: -1.22 (0.16), residues: 999 loop : -3.39 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 273 TYR 0.023 0.002 TYR N 114 PHE 0.033 0.002 PHE S 99 TRP 0.043 0.002 TRP F 479 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00300 (26790) covalent geometry : angle 0.76803 (36429) SS BOND : bond 0.00433 ( 45) SS BOND : angle 1.64531 ( 90) hydrogen bonds : bond 0.03682 ( 779) hydrogen bonds : angle 6.03447 ( 2226) Misc. bond : bond 0.00038 ( 4) link_ALPHA1-2 : bond 0.00317 ( 9) link_ALPHA1-2 : angle 1.58932 ( 27) link_ALPHA1-3 : bond 0.01091 ( 12) link_ALPHA1-3 : angle 1.56529 ( 36) link_ALPHA1-6 : bond 0.00705 ( 9) link_ALPHA1-6 : angle 1.61651 ( 27) link_BETA1-4 : bond 0.00983 ( 39) link_BETA1-4 : angle 2.27376 ( 117) link_NAG-ASN : bond 0.00764 ( 54) link_NAG-ASN : angle 3.89796 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 589 time to evaluate : 0.997 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: A 591 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: A 629 MET cc_start: 0.5877 (mmp) cc_final: 0.5318 (mmp) REVERT: B 589 ASP cc_start: 0.8725 (m-30) cc_final: 0.8453 (m-30) REVERT: B 620 ASN cc_start: 0.7811 (t0) cc_final: 0.7532 (p0) REVERT: C 589 ASP cc_start: 0.9053 (m-30) cc_final: 0.7974 (m-30) REVERT: C 620 ASN cc_start: 0.7852 (t0) cc_final: 0.7508 (p0) REVERT: D 95 MET cc_start: 0.7831 (ttp) cc_final: 0.7204 (ttp) REVERT: D 423 ILE cc_start: 0.8535 (mt) cc_final: 0.7741 (mt) REVERT: D 463 ASN cc_start: 0.7876 (p0) cc_final: 0.7444 (p0) REVERT: E 95 MET cc_start: 0.7806 (ttp) cc_final: 0.7102 (ttp) REVERT: E 477 ASP cc_start: 0.7755 (t70) cc_final: 0.7449 (t0) REVERT: F 327 ARG cc_start: 0.6644 (mtt90) cc_final: 0.6307 (mtm180) REVERT: F 423 ILE cc_start: 0.8817 (mt) cc_final: 0.8456 (mt) REVERT: G 79 SER cc_start: 0.8342 (m) cc_final: 0.7509 (p) REVERT: G 96 LEU cc_start: 0.7569 (mt) cc_final: 0.7318 (mt) REVERT: H 78 ASP cc_start: 0.7972 (m-30) cc_final: 0.7748 (m-30) REVERT: H 79 SER cc_start: 0.8342 (m) cc_final: 0.7565 (p) REVERT: I 79 SER cc_start: 0.8255 (m) cc_final: 0.7721 (p) REVERT: I 92 GLU cc_start: 0.7785 (tt0) cc_final: 0.7373 (tm-30) REVERT: J 46 GLU cc_start: 0.8739 (tp30) cc_final: 0.8531 (tp30) REVERT: J 51 PHE cc_start: 0.7613 (t80) cc_final: 0.7060 (t80) REVERT: J 76 THR cc_start: 0.8164 (p) cc_final: 0.7490 (p) REVERT: J 78 THR cc_start: 0.8142 (p) cc_final: 0.7680 (p) REVERT: J 81 MET cc_start: 0.7870 (tmm) cc_final: 0.7472 (tmm) REVERT: J 90 ASP cc_start: 0.6009 (m-30) cc_final: 0.5364 (m-30) REVERT: L 55 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6512 (mm-30) REVERT: L 76 THR cc_start: 0.7977 (p) cc_final: 0.7627 (p) REVERT: L 88 SER cc_start: 0.6502 (m) cc_final: 0.6094 (t) REVERT: L 95 TYR cc_start: 0.7716 (m-80) cc_final: 0.7423 (m-80) REVERT: L 107 THR cc_start: 0.6890 (m) cc_final: 0.6634 (m) REVERT: M 48 LEU cc_start: 0.7468 (pp) cc_final: 0.7128 (pp) REVERT: M 93 TRP cc_start: 0.7907 (t-100) cc_final: 0.7485 (t60) REVERT: M 99 THR cc_start: 0.7830 (p) cc_final: 0.7599 (p) REVERT: M 101 GLN cc_start: 0.8494 (tt0) cc_final: 0.8293 (tt0) REVERT: N 46 GLU cc_start: 0.8827 (tp30) cc_final: 0.8538 (tp30) REVERT: N 90 ASP cc_start: 0.6262 (m-30) cc_final: 0.5664 (m-30) REVERT: N 107 THR cc_start: 0.6956 (m) cc_final: 0.6665 (m) REVERT: O 50 ILE cc_start: 0.7107 (mt) cc_final: 0.6876 (mt) REVERT: O 77 ILE cc_start: 0.6675 (tp) cc_final: 0.6356 (tt) REVERT: O 99 THR cc_start: 0.7555 (p) cc_final: 0.7186 (p) REVERT: O 109 LEU cc_start: 0.7482 (tp) cc_final: 0.6681 (tp) REVERT: P 122 TRP cc_start: 0.8667 (m100) cc_final: 0.8298 (m100) REVERT: Q 2 ILE cc_start: 0.9312 (mm) cc_final: 0.9057 (mm) REVERT: Q 70 THR cc_start: 0.7173 (p) cc_final: 0.6653 (p) REVERT: Q 78 ASN cc_start: 0.8709 (t0) cc_final: 0.7598 (t0) REVERT: R 111 LEU cc_start: 0.9105 (mm) cc_final: 0.8481 (mt) REVERT: S 2 ILE cc_start: 0.8913 (mm) cc_final: 0.8556 (mm) REVERT: S 24 ARG cc_start: 0.7179 (mtp85) cc_final: 0.6756 (mtp85) REVERT: S 66 SER cc_start: 0.8469 (t) cc_final: 0.8112 (m) REVERT: S 78 ASN cc_start: 0.8292 (t0) cc_final: 0.7206 (t0) REVERT: T 111 LEU cc_start: 0.9191 (mm) cc_final: 0.8664 (mt) REVERT: T 122 TRP cc_start: 0.8722 (m100) cc_final: 0.7861 (m100) REVERT: U 23 CYS cc_start: 0.2403 (p) cc_final: 0.1726 (p) REVERT: U 36 TRP cc_start: 0.7136 (m100) cc_final: 0.6381 (m100) REVERT: U 38 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7735 (tm-30) REVERT: U 66 SER cc_start: 0.8753 (t) cc_final: 0.8297 (m) REVERT: U 78 ASN cc_start: 0.8496 (t0) cc_final: 0.8063 (t0) outliers start: 6 outliers final: 0 residues processed: 590 average time/residue: 0.1598 time to fit residues: 152.5576 Evaluate side-chains 446 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 317 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 300 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 126 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN F 99 ASN F 216 HIS G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN M 7 GLN M 55 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 HIS ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN S 27 GLN S 32 ASN S 90 GLN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN U 101 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100162 restraints weight = 50373.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102155 restraints weight = 29988.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102722 restraints weight = 23917.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103319 restraints weight = 20091.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103809 restraints weight = 18432.078| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26962 Z= 0.171 Angle : 0.847 17.163 36888 Z= 0.411 Chirality : 0.051 0.347 4503 Planarity : 0.006 0.106 4458 Dihedral : 8.866 59.689 5931 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.56 % Favored : 89.04 % Rotamer: Outliers : 0.11 % Allowed : 1.63 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.33 (0.13), residues: 3183 helix: -0.55 (0.26), residues: 387 sheet: -1.26 (0.16), residues: 1002 loop : -3.32 (0.12), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 273 TYR 0.026 0.002 TYR D 484 PHE 0.032 0.002 PHE T 63 TRP 0.026 0.002 TRP K 93 HIS 0.007 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00378 (26790) covalent geometry : angle 0.78313 (36429) SS BOND : bond 0.00530 ( 45) SS BOND : angle 1.70299 ( 90) hydrogen bonds : bond 0.03764 ( 779) hydrogen bonds : angle 6.00610 ( 2226) Misc. bond : bond 0.00030 ( 4) link_ALPHA1-2 : bond 0.00289 ( 9) link_ALPHA1-2 : angle 1.67410 ( 27) link_ALPHA1-3 : bond 0.00954 ( 12) link_ALPHA1-3 : angle 1.70561 ( 36) link_ALPHA1-6 : bond 0.00622 ( 9) link_ALPHA1-6 : angle 1.64055 ( 27) link_BETA1-4 : bond 0.00947 ( 39) link_BETA1-4 : angle 2.36468 ( 117) link_NAG-ASN : bond 0.00769 ( 54) link_NAG-ASN : angle 4.25147 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 559 time to evaluate : 0.915 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: A 620 ASN cc_start: 0.7550 (p0) cc_final: 0.7213 (t0) REVERT: A 629 MET cc_start: 0.6282 (mmp) cc_final: 0.5601 (mmp) REVERT: B 589 ASP cc_start: 0.8692 (m-30) cc_final: 0.8142 (m-30) REVERT: B 620 ASN cc_start: 0.7928 (t0) cc_final: 0.7452 (p0) REVERT: B 629 MET cc_start: 0.7225 (mmt) cc_final: 0.6490 (mmp) REVERT: C 589 ASP cc_start: 0.9003 (m-30) cc_final: 0.7919 (m-30) REVERT: C 620 ASN cc_start: 0.7881 (t0) cc_final: 0.7525 (p0) REVERT: D 95 MET cc_start: 0.7704 (ttp) cc_final: 0.6960 (ttp) REVERT: D 100 MET cc_start: 0.8414 (mtp) cc_final: 0.8193 (mtp) REVERT: D 104 MET cc_start: 0.8468 (tpp) cc_final: 0.8147 (tpp) REVERT: D 423 ILE cc_start: 0.8604 (mt) cc_final: 0.7849 (mt) REVERT: D 463 ASN cc_start: 0.8009 (p0) cc_final: 0.7597 (p0) REVERT: E 95 MET cc_start: 0.7883 (ttp) cc_final: 0.7236 (ttp) REVERT: E 106 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7694 (tm-30) REVERT: E 477 ASP cc_start: 0.7867 (t70) cc_final: 0.7576 (t0) REVERT: F 107 ASP cc_start: 0.8363 (t70) cc_final: 0.8140 (t70) REVERT: F 423 ILE cc_start: 0.8963 (mt) cc_final: 0.8693 (mt) REVERT: H 78 ASP cc_start: 0.8131 (m-30) cc_final: 0.7831 (m-30) REVERT: H 79 SER cc_start: 0.8426 (m) cc_final: 0.7677 (p) REVERT: I 71 ILE cc_start: 0.8737 (mm) cc_final: 0.8529 (mm) REVERT: I 79 SER cc_start: 0.8273 (m) cc_final: 0.7767 (p) REVERT: I 92 GLU cc_start: 0.7812 (tt0) cc_final: 0.7434 (tm-30) REVERT: J 10 GLU cc_start: 0.8385 (tp30) cc_final: 0.8163 (tp30) REVERT: J 24 VAL cc_start: 0.8247 (t) cc_final: 0.8034 (t) REVERT: J 46 GLU cc_start: 0.8853 (tp30) cc_final: 0.8512 (tp30) REVERT: J 67 ARG cc_start: 0.3800 (ptt180) cc_final: 0.3403 (ptt180) REVERT: J 78 THR cc_start: 0.8505 (p) cc_final: 0.8286 (p) REVERT: J 80 TYR cc_start: 0.6806 (m-10) cc_final: 0.6450 (m-10) REVERT: J 90 ASP cc_start: 0.5957 (m-30) cc_final: 0.5756 (m-30) REVERT: K 93 TRP cc_start: 0.7559 (t-100) cc_final: 0.7225 (t-100) REVERT: L 55 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6787 (mm-30) REVERT: L 76 THR cc_start: 0.7844 (p) cc_final: 0.7520 (p) REVERT: L 87 ARG cc_start: 0.8341 (mmt90) cc_final: 0.8082 (mmt90) REVERT: L 88 SER cc_start: 0.6682 (m) cc_final: 0.6213 (t) REVERT: L 107 THR cc_start: 0.6917 (m) cc_final: 0.6536 (p) REVERT: M 55 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8359 (mp10) REVERT: M 93 TRP cc_start: 0.8015 (t-100) cc_final: 0.7631 (t60) REVERT: M 101 GLN cc_start: 0.8506 (tt0) cc_final: 0.8078 (tt0) REVERT: N 46 GLU cc_start: 0.8868 (tp30) cc_final: 0.8584 (tp30) REVERT: N 90 ASP cc_start: 0.6247 (m-30) cc_final: 0.5662 (m-30) REVERT: O 50 ILE cc_start: 0.7267 (mt) cc_final: 0.7053 (mt) REVERT: O 109 LEU cc_start: 0.7522 (tp) cc_final: 0.7309 (tp) REVERT: P 122 TRP cc_start: 0.8704 (m100) cc_final: 0.8322 (m100) REVERT: Q 2 ILE cc_start: 0.9256 (mm) cc_final: 0.8980 (mm) REVERT: Q 38 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7379 (tm-30) REVERT: Q 66 SER cc_start: 0.8181 (t) cc_final: 0.7902 (m) REVERT: Q 78 ASN cc_start: 0.8711 (t0) cc_final: 0.7503 (t0) REVERT: S 24 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7096 (mtp85) REVERT: S 66 SER cc_start: 0.8466 (t) cc_final: 0.8029 (m) REVERT: S 78 ASN cc_start: 0.8354 (t0) cc_final: 0.7822 (t0) REVERT: S 84 PHE cc_start: 0.7427 (m-10) cc_final: 0.7113 (m-80) REVERT: T 111 LEU cc_start: 0.9271 (mm) cc_final: 0.8823 (mt) REVERT: T 122 TRP cc_start: 0.8746 (m100) cc_final: 0.8079 (m100) REVERT: U 23 CYS cc_start: 0.2316 (p) cc_final: 0.1784 (p) REVERT: U 36 TRP cc_start: 0.7231 (m100) cc_final: 0.6438 (m100) REVERT: U 38 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7844 (tm-30) REVERT: U 66 SER cc_start: 0.8752 (t) cc_final: 0.8328 (m) REVERT: U 78 ASN cc_start: 0.8494 (t0) cc_final: 0.7371 (t0) outliers start: 3 outliers final: 0 residues processed: 560 average time/residue: 0.1586 time to fit residues: 143.7493 Evaluate side-chains 436 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 125 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 262 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN M 7 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN O 7 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 HIS R 51 GLN S 32 ASN S 90 GLN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN T 124 GLN U 32 ASN U 101 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.122545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098043 restraints weight = 50569.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100317 restraints weight = 32127.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101823 restraints weight = 22857.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103888 restraints weight = 18779.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104292 restraints weight = 15602.857| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26962 Z= 0.182 Angle : 0.842 13.310 36888 Z= 0.413 Chirality : 0.051 0.344 4503 Planarity : 0.006 0.090 4458 Dihedral : 8.498 56.361 5931 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.03 % Favored : 88.53 % Rotamer: Outliers : 0.23 % Allowed : 1.67 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.13), residues: 3183 helix: -0.36 (0.26), residues: 369 sheet: -1.16 (0.16), residues: 1011 loop : -3.32 (0.12), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 273 TYR 0.027 0.002 TYR E 484 PHE 0.025 0.002 PHE M 64 TRP 0.024 0.002 TRP R 122 HIS 0.007 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00404 (26790) covalent geometry : angle 0.78739 (36429) SS BOND : bond 0.00672 ( 45) SS BOND : angle 1.80401 ( 90) hydrogen bonds : bond 0.03787 ( 779) hydrogen bonds : angle 5.91062 ( 2226) Misc. bond : bond 0.00493 ( 4) link_ALPHA1-2 : bond 0.00318 ( 9) link_ALPHA1-2 : angle 1.67327 ( 27) link_ALPHA1-3 : bond 0.00914 ( 12) link_ALPHA1-3 : angle 1.68179 ( 36) link_ALPHA1-6 : bond 0.00606 ( 9) link_ALPHA1-6 : angle 1.72932 ( 27) link_BETA1-4 : bond 0.01001 ( 39) link_BETA1-4 : angle 2.38515 ( 117) link_NAG-ASN : bond 0.00689 ( 54) link_NAG-ASN : angle 3.82527 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 558 time to evaluate : 1.027 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: A 591 GLN cc_start: 0.8442 (pm20) cc_final: 0.7927 (pm20) REVERT: A 629 MET cc_start: 0.6569 (mmp) cc_final: 0.6031 (mmp) REVERT: B 620 ASN cc_start: 0.7979 (t0) cc_final: 0.7611 (p0) REVERT: B 629 MET cc_start: 0.7251 (mmt) cc_final: 0.6505 (mmp) REVERT: C 589 ASP cc_start: 0.9003 (m-30) cc_final: 0.7940 (m-30) REVERT: C 590 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8545 (mm-40) REVERT: D 95 MET cc_start: 0.8009 (ttp) cc_final: 0.7122 (ttp) REVERT: D 100 MET cc_start: 0.8364 (mtp) cc_final: 0.8132 (mtp) REVERT: D 104 MET cc_start: 0.8790 (tpp) cc_final: 0.7988 (tpp) REVERT: D 423 ILE cc_start: 0.8580 (mt) cc_final: 0.7882 (mt) REVERT: D 463 ASN cc_start: 0.7934 (p0) cc_final: 0.7632 (p0) REVERT: E 106 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7690 (tm-30) REVERT: E 477 ASP cc_start: 0.7989 (t70) cc_final: 0.7752 (t0) REVERT: F 104 MET cc_start: 0.8254 (tpt) cc_final: 0.7966 (tpt) REVERT: F 194 ILE cc_start: 0.8932 (mm) cc_final: 0.8621 (tt) REVERT: F 423 ILE cc_start: 0.8969 (mt) cc_final: 0.8752 (mt) REVERT: H 79 SER cc_start: 0.8407 (m) cc_final: 0.7601 (p) REVERT: I 71 ILE cc_start: 0.8736 (mm) cc_final: 0.8532 (mm) REVERT: I 79 SER cc_start: 0.8231 (m) cc_final: 0.7719 (p) REVERT: I 92 GLU cc_start: 0.7759 (tt0) cc_final: 0.7370 (tm-30) REVERT: J 46 GLU cc_start: 0.8882 (tp30) cc_final: 0.8406 (tp30) REVERT: J 67 ARG cc_start: 0.3683 (ptt180) cc_final: 0.3381 (ptt180) REVERT: J 78 THR cc_start: 0.8615 (p) cc_final: 0.8393 (p) REVERT: J 80 TYR cc_start: 0.6945 (m-10) cc_final: 0.6457 (m-10) REVERT: J 81 MET cc_start: 0.7798 (tmm) cc_final: 0.7543 (tmm) REVERT: J 90 ASP cc_start: 0.6040 (m-30) cc_final: 0.5776 (m-30) REVERT: K 93 TRP cc_start: 0.7629 (t-100) cc_final: 0.7350 (t-100) REVERT: L 55 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6906 (mm-30) REVERT: L 87 ARG cc_start: 0.8348 (mmt90) cc_final: 0.8095 (mmt90) REVERT: L 88 SER cc_start: 0.5902 (m) cc_final: 0.5348 (t) REVERT: L 107 THR cc_start: 0.6832 (m) cc_final: 0.6414 (m) REVERT: M 32 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8350 (ttpt) REVERT: M 93 TRP cc_start: 0.7959 (t-100) cc_final: 0.7600 (t-100) REVERT: M 101 GLN cc_start: 0.8461 (tt0) cc_final: 0.8045 (tt0) REVERT: N 10 GLU cc_start: 0.8174 (tp30) cc_final: 0.7500 (tp30) REVERT: N 46 GLU cc_start: 0.8816 (tp30) cc_final: 0.8575 (tp30) REVERT: N 90 ASP cc_start: 0.6215 (m-30) cc_final: 0.5555 (m-30) REVERT: N 107 THR cc_start: 0.6898 (m) cc_final: 0.6599 (p) REVERT: O 18 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7938 (ptmm) REVERT: O 50 ILE cc_start: 0.7320 (mt) cc_final: 0.7100 (mt) REVERT: O 99 THR cc_start: 0.7528 (p) cc_final: 0.6995 (p) REVERT: P 122 TRP cc_start: 0.8677 (m100) cc_final: 0.8243 (m100) REVERT: Q 2 ILE cc_start: 0.9020 (mm) cc_final: 0.8782 (mm) REVERT: Q 38 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7459 (tm-30) REVERT: Q 66 SER cc_start: 0.8048 (t) cc_final: 0.7837 (m) REVERT: Q 78 ASN cc_start: 0.8690 (t0) cc_final: 0.8024 (t0) REVERT: S 24 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6875 (mtp85) REVERT: S 66 SER cc_start: 0.8507 (t) cc_final: 0.8205 (m) REVERT: S 78 ASN cc_start: 0.8358 (t0) cc_final: 0.7338 (t0) REVERT: S 84 PHE cc_start: 0.7464 (m-10) cc_final: 0.7134 (m-80) REVERT: T 111 LEU cc_start: 0.9303 (mm) cc_final: 0.8820 (mt) REVERT: T 122 TRP cc_start: 0.8779 (m100) cc_final: 0.8107 (m100) REVERT: U 38 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7879 (tm-30) REVERT: U 66 SER cc_start: 0.8534 (t) cc_final: 0.8185 (m) REVERT: U 78 ASN cc_start: 0.8503 (t0) cc_final: 0.8079 (t0) outliers start: 6 outliers final: 0 residues processed: 563 average time/residue: 0.1590 time to fit residues: 144.5071 Evaluate side-chains 442 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 101 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN M 7 GLN M 55 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN N 101 ASN O 7 GLN O 101 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 HIS R 51 GLN S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN T 124 GLN U 6 GLN U 32 ASN ** U 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.123250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100161 restraints weight = 50411.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101049 restraints weight = 32900.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102012 restraints weight = 28369.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.102760 restraints weight = 21932.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103815 restraints weight = 19326.228| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26962 Z= 0.184 Angle : 0.856 14.435 36888 Z= 0.419 Chirality : 0.052 0.345 4503 Planarity : 0.006 0.110 4458 Dihedral : 9.514 128.610 5931 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.44 % Favored : 88.16 % Rotamer: Outliers : 0.15 % Allowed : 1.33 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.13), residues: 3183 helix: -0.31 (0.27), residues: 369 sheet: -1.21 (0.16), residues: 1029 loop : -3.30 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 273 TYR 0.046 0.002 TYR D 484 PHE 0.032 0.002 PHE T 63 TRP 0.021 0.002 TRP R 122 HIS 0.008 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00415 (26790) covalent geometry : angle 0.80036 (36429) SS BOND : bond 0.00548 ( 45) SS BOND : angle 1.69936 ( 90) hydrogen bonds : bond 0.03819 ( 779) hydrogen bonds : angle 5.89937 ( 2226) Misc. bond : bond 0.00143 ( 4) link_ALPHA1-2 : bond 0.00293 ( 9) link_ALPHA1-2 : angle 1.67133 ( 27) link_ALPHA1-3 : bond 0.00887 ( 12) link_ALPHA1-3 : angle 1.57466 ( 36) link_ALPHA1-6 : bond 0.00612 ( 9) link_ALPHA1-6 : angle 1.70634 ( 27) link_BETA1-4 : bond 0.00913 ( 39) link_BETA1-4 : angle 2.36498 ( 117) link_NAG-ASN : bond 0.00704 ( 54) link_NAG-ASN : angle 3.97438 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 549 time to evaluate : 0.960 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: A 587 LEU cc_start: 0.9151 (mm) cc_final: 0.8404 (mm) REVERT: A 591 GLN cc_start: 0.8601 (pm20) cc_final: 0.7966 (pm20) REVERT: A 620 ASN cc_start: 0.7484 (p0) cc_final: 0.7198 (t0) REVERT: A 629 MET cc_start: 0.6623 (mmp) cc_final: 0.6114 (mmp) REVERT: B 620 ASN cc_start: 0.8110 (t0) cc_final: 0.7641 (p0) REVERT: C 589 ASP cc_start: 0.8985 (m-30) cc_final: 0.7888 (m-30) REVERT: C 643 TYR cc_start: 0.7925 (m-80) cc_final: 0.7568 (m-80) REVERT: D 95 MET cc_start: 0.8099 (ttp) cc_final: 0.6658 (mmm) REVERT: D 100 MET cc_start: 0.8445 (mtp) cc_final: 0.8178 (mtp) REVERT: D 104 MET cc_start: 0.8835 (tpp) cc_final: 0.8444 (tpp) REVERT: D 346 VAL cc_start: 0.8261 (t) cc_final: 0.8038 (p) REVERT: D 423 ILE cc_start: 0.8563 (mt) cc_final: 0.7827 (mt) REVERT: D 463 ASN cc_start: 0.8159 (p0) cc_final: 0.7875 (p0) REVERT: E 104 MET cc_start: 0.8682 (tpp) cc_final: 0.8284 (tpp) REVERT: E 106 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7709 (tm-30) REVERT: E 217 TYR cc_start: 0.7083 (m-10) cc_final: 0.6773 (m-80) REVERT: E 477 ASP cc_start: 0.7938 (t70) cc_final: 0.7738 (t0) REVERT: F 104 MET cc_start: 0.8311 (tpt) cc_final: 0.8066 (tpt) REVERT: F 107 ASP cc_start: 0.8345 (t70) cc_final: 0.8058 (t0) REVERT: G 78 ASP cc_start: 0.7987 (m-30) cc_final: 0.7745 (m-30) REVERT: G 79 SER cc_start: 0.8266 (m) cc_final: 0.7515 (p) REVERT: H 78 ASP cc_start: 0.8097 (m-30) cc_final: 0.7885 (m-30) REVERT: H 79 SER cc_start: 0.8421 (m) cc_final: 0.7613 (p) REVERT: I 79 SER cc_start: 0.8255 (m) cc_final: 0.7794 (p) REVERT: J 10 GLU cc_start: 0.8074 (tp30) cc_final: 0.7806 (tp30) REVERT: J 46 GLU cc_start: 0.8863 (tp30) cc_final: 0.8399 (tp30) REVERT: J 67 ARG cc_start: 0.3966 (ptt180) cc_final: 0.3674 (ptt180) REVERT: J 78 THR cc_start: 0.8643 (p) cc_final: 0.8307 (p) REVERT: J 80 TYR cc_start: 0.6975 (m-10) cc_final: 0.6475 (m-10) REVERT: J 81 MET cc_start: 0.7759 (tmm) cc_final: 0.7502 (tmm) REVERT: J 90 ASP cc_start: 0.6052 (m-30) cc_final: 0.5801 (m-30) REVERT: K 55 GLN cc_start: 0.8086 (mp-120) cc_final: 0.7795 (mp10) REVERT: K 93 TRP cc_start: 0.7602 (t-100) cc_final: 0.7353 (t-100) REVERT: L 55 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6889 (mm-30) REVERT: L 78 THR cc_start: 0.8156 (p) cc_final: 0.7920 (t) REVERT: L 87 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8231 (mmt90) REVERT: L 90 ASP cc_start: 0.5732 (m-30) cc_final: 0.5317 (m-30) REVERT: L 107 THR cc_start: 0.6934 (m) cc_final: 0.6593 (m) REVERT: M 93 TRP cc_start: 0.7977 (t-100) cc_final: 0.7551 (t-100) REVERT: M 101 GLN cc_start: 0.8407 (tt0) cc_final: 0.8048 (tt0) REVERT: N 10 GLU cc_start: 0.8345 (tp30) cc_final: 0.8046 (tp30) REVERT: N 76 THR cc_start: 0.8064 (p) cc_final: 0.7830 (p) REVERT: N 78 THR cc_start: 0.8207 (p) cc_final: 0.7999 (p) REVERT: N 90 ASP cc_start: 0.6244 (m-30) cc_final: 0.5627 (m-30) REVERT: O 99 THR cc_start: 0.7651 (p) cc_final: 0.7090 (p) REVERT: P 122 TRP cc_start: 0.8625 (m100) cc_final: 0.8234 (m100) REVERT: Q 38 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7532 (tm-30) REVERT: Q 66 SER cc_start: 0.8154 (t) cc_final: 0.7948 (m) REVERT: Q 70 THR cc_start: 0.7156 (p) cc_final: 0.6886 (p) REVERT: Q 78 ASN cc_start: 0.8702 (t0) cc_final: 0.7877 (t0) REVERT: S 24 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6934 (mtp85) REVERT: S 78 ASN cc_start: 0.8425 (t0) cc_final: 0.7366 (t0) REVERT: T 111 LEU cc_start: 0.9299 (mm) cc_final: 0.8808 (mt) REVERT: T 122 TRP cc_start: 0.8756 (m100) cc_final: 0.8139 (m100) REVERT: U 38 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7919 (tm-30) REVERT: U 66 SER cc_start: 0.8562 (t) cc_final: 0.8211 (m) REVERT: U 78 ASN cc_start: 0.8509 (t0) cc_final: 0.7394 (t0) outliers start: 4 outliers final: 0 residues processed: 552 average time/residue: 0.1578 time to fit residues: 141.2434 Evaluate side-chains 436 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 168 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN M 55 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN N 104 ASN O 7 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 GLN S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN U 32 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.126354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103252 restraints weight = 49679.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104368 restraints weight = 32119.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105396 restraints weight = 26654.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.106147 restraints weight = 20391.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.106479 restraints weight = 18285.016| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26962 Z= 0.147 Angle : 0.820 13.326 36888 Z= 0.404 Chirality : 0.050 0.353 4503 Planarity : 0.006 0.088 4458 Dihedral : 9.048 123.271 5931 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.46 % Favored : 90.14 % Rotamer: Outliers : 0.15 % Allowed : 0.64 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.13), residues: 3183 helix: -0.20 (0.27), residues: 366 sheet: -0.99 (0.16), residues: 993 loop : -3.28 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 273 TYR 0.026 0.002 TYR C 643 PHE 0.028 0.002 PHE M 64 TRP 0.023 0.002 TRP N 47 HIS 0.007 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00327 (26790) covalent geometry : angle 0.76424 (36429) SS BOND : bond 0.00511 ( 45) SS BOND : angle 1.61254 ( 90) hydrogen bonds : bond 0.03573 ( 779) hydrogen bonds : angle 5.74845 ( 2226) Misc. bond : bond 0.00026 ( 4) link_ALPHA1-2 : bond 0.00286 ( 9) link_ALPHA1-2 : angle 1.59953 ( 27) link_ALPHA1-3 : bond 0.00944 ( 12) link_ALPHA1-3 : angle 1.35285 ( 36) link_ALPHA1-6 : bond 0.00699 ( 9) link_ALPHA1-6 : angle 1.59669 ( 27) link_BETA1-4 : bond 0.00942 ( 39) link_BETA1-4 : angle 2.25820 ( 117) link_NAG-ASN : bond 0.00662 ( 54) link_NAG-ASN : angle 3.91697 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 550 time to evaluate : 1.015 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: A 587 LEU cc_start: 0.9070 (mm) cc_final: 0.8789 (mt) REVERT: A 620 ASN cc_start: 0.7475 (p0) cc_final: 0.7078 (t0) REVERT: A 629 MET cc_start: 0.6276 (mmp) cc_final: 0.5814 (mmp) REVERT: B 620 ASN cc_start: 0.8136 (t0) cc_final: 0.7678 (p0) REVERT: C 523 LEU cc_start: 0.8727 (pt) cc_final: 0.8326 (pp) REVERT: C 589 ASP cc_start: 0.8940 (m-30) cc_final: 0.7913 (m-30) REVERT: C 620 ASN cc_start: 0.7982 (t0) cc_final: 0.7539 (p0) REVERT: C 643 TYR cc_start: 0.7937 (m-80) cc_final: 0.7498 (m-80) REVERT: D 95 MET cc_start: 0.7928 (ttp) cc_final: 0.7201 (ttp) REVERT: D 104 MET cc_start: 0.8815 (tpp) cc_final: 0.8436 (tpp) REVERT: D 423 ILE cc_start: 0.8507 (mt) cc_final: 0.7927 (mm) REVERT: D 463 ASN cc_start: 0.8091 (p0) cc_final: 0.7746 (p0) REVERT: E 104 MET cc_start: 0.8697 (tpp) cc_final: 0.8325 (tpp) REVERT: F 40 TYR cc_start: 0.8436 (t80) cc_final: 0.8227 (t80) REVERT: F 107 ASP cc_start: 0.8366 (t70) cc_final: 0.8131 (t0) REVERT: G 79 SER cc_start: 0.8338 (m) cc_final: 0.7588 (p) REVERT: H 78 ASP cc_start: 0.8029 (m-30) cc_final: 0.7775 (m-30) REVERT: H 79 SER cc_start: 0.8430 (m) cc_final: 0.7638 (p) REVERT: I 79 SER cc_start: 0.8234 (m) cc_final: 0.7811 (p) REVERT: J 10 GLU cc_start: 0.8302 (tp30) cc_final: 0.7921 (tp30) REVERT: J 46 GLU cc_start: 0.8776 (tp30) cc_final: 0.8467 (tp30) REVERT: J 67 ARG cc_start: 0.3917 (ptt180) cc_final: 0.3584 (ptt180) REVERT: J 78 THR cc_start: 0.8720 (p) cc_final: 0.8365 (p) REVERT: J 80 TYR cc_start: 0.6949 (m-10) cc_final: 0.6435 (m-10) REVERT: J 81 MET cc_start: 0.7706 (tmm) cc_final: 0.7469 (tmm) REVERT: K 93 TRP cc_start: 0.7707 (t-100) cc_final: 0.7318 (t-100) REVERT: L 10 GLU cc_start: 0.8246 (tp30) cc_final: 0.7979 (tp30) REVERT: L 23 LYS cc_start: 0.8172 (tptp) cc_final: 0.7658 (tptm) REVERT: L 55 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6972 (mm-30) REVERT: L 78 THR cc_start: 0.8117 (p) cc_final: 0.7461 (p) REVERT: L 80 TYR cc_start: 0.6532 (m-10) cc_final: 0.5891 (m-10) REVERT: L 85 SER cc_start: 0.7271 (t) cc_final: 0.6816 (p) REVERT: L 88 SER cc_start: 0.6140 (m) cc_final: 0.5678 (t) REVERT: L 90 ASP cc_start: 0.5687 (m-30) cc_final: 0.5356 (m-30) REVERT: L 107 THR cc_start: 0.6907 (m) cc_final: 0.6499 (m) REVERT: M 93 TRP cc_start: 0.7892 (t-100) cc_final: 0.7534 (t60) REVERT: N 90 ASP cc_start: 0.6174 (m-30) cc_final: 0.5625 (m-30) REVERT: O 99 THR cc_start: 0.7331 (p) cc_final: 0.6839 (p) REVERT: P 122 TRP cc_start: 0.8710 (m100) cc_final: 0.8311 (m100) REVERT: Q 2 ILE cc_start: 0.8896 (mm) cc_final: 0.8643 (mm) REVERT: Q 38 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7758 (tm-30) REVERT: Q 78 ASN cc_start: 0.8717 (t0) cc_final: 0.7901 (t0) REVERT: S 78 ASN cc_start: 0.8408 (t0) cc_final: 0.7311 (t0) REVERT: S 80 GLN cc_start: 0.8031 (mm110) cc_final: 0.7772 (mm110) REVERT: T 111 LEU cc_start: 0.9260 (mm) cc_final: 0.8754 (mt) REVERT: T 122 TRP cc_start: 0.8710 (m100) cc_final: 0.8006 (m100) REVERT: U 38 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7845 (tm-30) REVERT: U 66 SER cc_start: 0.8679 (t) cc_final: 0.8468 (m) REVERT: U 78 ASN cc_start: 0.8518 (t0) cc_final: 0.8108 (t0) outliers start: 4 outliers final: 0 residues processed: 553 average time/residue: 0.1531 time to fit residues: 137.5288 Evaluate side-chains 441 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 287 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 243 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 73 ASN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN M 55 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN N 101 ASN O 7 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN U 32 ASN ** U 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.125158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100633 restraints weight = 50078.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104227 restraints weight = 32478.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105080 restraints weight = 21845.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105345 restraints weight = 18700.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105633 restraints weight = 17870.521| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26962 Z= 0.160 Angle : 0.838 14.009 36888 Z= 0.411 Chirality : 0.050 0.347 4503 Planarity : 0.006 0.105 4458 Dihedral : 8.892 125.004 5931 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.52 % Favored : 89.07 % Rotamer: Outliers : 0.11 % Allowed : 0.38 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.13), residues: 3183 helix: -0.15 (0.27), residues: 366 sheet: -0.91 (0.16), residues: 1005 loop : -3.30 (0.12), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 12 TYR 0.036 0.002 TYR A 643 PHE 0.029 0.002 PHE P 63 TRP 0.043 0.002 TRP R 53 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00356 (26790) covalent geometry : angle 0.78079 (36429) SS BOND : bond 0.00518 ( 45) SS BOND : angle 1.63513 ( 90) hydrogen bonds : bond 0.03626 ( 779) hydrogen bonds : angle 5.69374 ( 2226) Misc. bond : bond 0.00032 ( 4) link_ALPHA1-2 : bond 0.00267 ( 9) link_ALPHA1-2 : angle 1.63364 ( 27) link_ALPHA1-3 : bond 0.00871 ( 12) link_ALPHA1-3 : angle 1.46822 ( 36) link_ALPHA1-6 : bond 0.00694 ( 9) link_ALPHA1-6 : angle 1.68824 ( 27) link_BETA1-4 : bond 0.00937 ( 39) link_BETA1-4 : angle 2.28732 ( 117) link_NAG-ASN : bond 0.00693 ( 54) link_NAG-ASN : angle 4.02221 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 529 time to evaluate : 0.981 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: A 629 MET cc_start: 0.6498 (mmp) cc_final: 0.6011 (mmp) REVERT: A 643 TYR cc_start: 0.8079 (m-80) cc_final: 0.7648 (m-80) REVERT: B 620 ASN cc_start: 0.8036 (t0) cc_final: 0.7616 (p0) REVERT: C 523 LEU cc_start: 0.8762 (pt) cc_final: 0.8358 (pp) REVERT: C 589 ASP cc_start: 0.8978 (m-30) cc_final: 0.7911 (m-30) REVERT: C 620 ASN cc_start: 0.7997 (t0) cc_final: 0.7550 (p0) REVERT: C 643 TYR cc_start: 0.8087 (m-80) cc_final: 0.7659 (m-80) REVERT: D 95 MET cc_start: 0.7982 (ttp) cc_final: 0.7195 (ttp) REVERT: D 104 MET cc_start: 0.8807 (tpp) cc_final: 0.8581 (tpp) REVERT: D 423 ILE cc_start: 0.8555 (mt) cc_final: 0.7991 (mm) REVERT: D 463 ASN cc_start: 0.8131 (p0) cc_final: 0.7770 (p0) REVERT: E 95 MET cc_start: 0.7804 (ttp) cc_final: 0.7155 (ttp) REVERT: E 104 MET cc_start: 0.8681 (tpp) cc_final: 0.8271 (tpp) REVERT: E 475 MET cc_start: 0.8266 (mmm) cc_final: 0.7934 (mmm) REVERT: E 477 ASP cc_start: 0.7924 (t70) cc_final: 0.7587 (t0) REVERT: F 40 TYR cc_start: 0.8447 (t80) cc_final: 0.8236 (t80) REVERT: G 78 ASP cc_start: 0.7961 (m-30) cc_final: 0.7736 (m-30) REVERT: G 79 SER cc_start: 0.8190 (m) cc_final: 0.7491 (p) REVERT: H 78 ASP cc_start: 0.8130 (m-30) cc_final: 0.7873 (m-30) REVERT: H 79 SER cc_start: 0.8410 (m) cc_final: 0.7625 (p) REVERT: I 79 SER cc_start: 0.8349 (m) cc_final: 0.7843 (p) REVERT: J 10 GLU cc_start: 0.8345 (tp30) cc_final: 0.8131 (tp30) REVERT: J 46 GLU cc_start: 0.8791 (tp30) cc_final: 0.8450 (tp30) REVERT: J 67 ARG cc_start: 0.4061 (ptt180) cc_final: 0.3747 (ptt180) REVERT: J 78 THR cc_start: 0.8705 (p) cc_final: 0.8296 (t) REVERT: J 80 TYR cc_start: 0.6884 (m-10) cc_final: 0.6574 (m-10) REVERT: J 81 MET cc_start: 0.7728 (tmm) cc_final: 0.7458 (tmm) REVERT: K 33 ASN cc_start: 0.7980 (m-40) cc_final: 0.7592 (m-40) REVERT: K 93 TRP cc_start: 0.7682 (t-100) cc_final: 0.7346 (t-100) REVERT: L 10 GLU cc_start: 0.8211 (tp30) cc_final: 0.7965 (tp30) REVERT: L 55 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7040 (mm-30) REVERT: L 81 MET cc_start: 0.7422 (tmm) cc_final: 0.6810 (tmm) REVERT: L 90 ASP cc_start: 0.5758 (m-30) cc_final: 0.5435 (m-30) REVERT: L 107 THR cc_start: 0.7086 (m) cc_final: 0.6635 (m) REVERT: M 93 TRP cc_start: 0.7952 (t-100) cc_final: 0.7559 (t-100) REVERT: N 90 ASP cc_start: 0.6098 (m-30) cc_final: 0.5662 (m-30) REVERT: O 108 LYS cc_start: 0.8398 (ptmt) cc_final: 0.8042 (mmtm) REVERT: P 122 TRP cc_start: 0.8717 (m100) cc_final: 0.8322 (m100) REVERT: Q 38 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7816 (tm-30) REVERT: Q 78 ASN cc_start: 0.8714 (t0) cc_final: 0.7859 (t0) REVERT: S 23 CYS cc_start: 0.2779 (p) cc_final: 0.2179 (p) REVERT: S 24 ARG cc_start: 0.7175 (mtp85) cc_final: 0.6801 (mtp85) REVERT: S 78 ASN cc_start: 0.8430 (t0) cc_final: 0.7277 (t0) REVERT: T 111 LEU cc_start: 0.9279 (mm) cc_final: 0.8729 (mt) REVERT: T 122 TRP cc_start: 0.8736 (m100) cc_final: 0.8198 (m100) REVERT: U 38 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7859 (tm-30) REVERT: U 66 SER cc_start: 0.8630 (t) cc_final: 0.8421 (m) REVERT: U 78 ASN cc_start: 0.8462 (t0) cc_final: 0.8067 (t0) outliers start: 3 outliers final: 1 residues processed: 532 average time/residue: 0.1497 time to fit residues: 130.6224 Evaluate side-chains 436 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 435 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 288 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 463 ASN G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN K 55 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN M 55 GLN M 81 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN O 7 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN R 61 HIS S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN U 32 ASN ** U 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099759 restraints weight = 50205.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101506 restraints weight = 33858.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102500 restraints weight = 25865.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103030 restraints weight = 21305.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103333 restraints weight = 19690.746| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26962 Z= 0.177 Angle : 0.846 13.445 36888 Z= 0.415 Chirality : 0.051 0.342 4503 Planarity : 0.006 0.102 4458 Dihedral : 8.892 122.328 5931 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.74 % Favored : 88.85 % Rotamer: Outliers : 0.08 % Allowed : 0.61 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.13), residues: 3183 helix: -0.24 (0.26), residues: 375 sheet: -0.95 (0.16), residues: 1035 loop : -3.31 (0.12), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 273 TYR 0.034 0.002 TYR A 643 PHE 0.033 0.002 PHE T 63 TRP 0.036 0.002 TRP T 53 HIS 0.009 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00397 (26790) covalent geometry : angle 0.78854 (36429) SS BOND : bond 0.00526 ( 45) SS BOND : angle 1.64875 ( 90) hydrogen bonds : bond 0.03690 ( 779) hydrogen bonds : angle 5.72606 ( 2226) Misc. bond : bond 0.00030 ( 4) link_ALPHA1-2 : bond 0.00277 ( 9) link_ALPHA1-2 : angle 1.66027 ( 27) link_ALPHA1-3 : bond 0.00840 ( 12) link_ALPHA1-3 : angle 1.49391 ( 36) link_ALPHA1-6 : bond 0.00693 ( 9) link_ALPHA1-6 : angle 1.68259 ( 27) link_BETA1-4 : bond 0.00920 ( 39) link_BETA1-4 : angle 2.33405 ( 117) link_NAG-ASN : bond 0.00665 ( 54) link_NAG-ASN : angle 4.04287 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.16 seconds wall clock time: 76 minutes 55.47 seconds (4615.47 seconds total)