Starting phenix.real_space_refine on Sun Sep 13 22:37:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_9038.cif Found real_map, /net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_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_2026/6edu_9038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_9038.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_9038.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_9038.cif" model { file = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_9038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6edu_9038/09_2026/6edu_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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 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 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 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 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 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 chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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 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 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 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 chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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 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 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 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 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 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 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 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 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 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: 5.62, per 1000 atoms: 0.21 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: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.96 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: 6.14 Time building geometry restraints manager: 3.34 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 - 17.80: 13975 17.80 - 35.60: 706 35.60 - 53.39: 213 53.39 - 71.19: 20 71.19 - 88.99: 11 Dihedral angle restraints: 14925 sinusoidal: 5655 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 14922 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.240 Find NCS groups from input model: 0.750 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: 0.000 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: 30.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 11.561 74.096 8844 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 are 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/Z covalent geometry : bond 0.00754 / 0.42 (26790) covalent geometry : angle 1.37278 / 0.78 (36429) SS BOND : bond 0.11121 / 6.92 ( 45) SS BOND : angle 5.01082 / 3.37 ( 90) hydrogen bonds : bond 0.17380 / 11.64 ( 779) hydrogen bonds : angle 9.28671 / 6.71 ( 2226) Misc. bond : bond 0.09519 / 5.00 ( 4) link_ALPHA1-2 : bond 0.00381 / 0.26 ( 9) link_ALPHA1-2 : angle 1.94706 / 1.28 ( 27) link_ALPHA1-3 : bond 0.00431 / 0.28 ( 12) link_ALPHA1-3 : angle 1.78128 / 1.11 ( 36) link_ALPHA1-6 : bond 0.00083 / 0.05 ( 9) link_ALPHA1-6 : angle 1.64353 / 1.11 ( 27) link_BETA1-4 : bond 0.01490 / 0.77 ( 39) link_BETA1-4 : angle 3.82396 / 2.63 ( 117) link_NAG-ASN : bond 0.01405 / 0.88 ( 54) link_NAG-ASN : angle 5.52766 / 4.18 ( 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 : 0.884 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: 0.6530 (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: 0.7148 (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: 0.7836 (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: 0.8024 (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: 0.8255 (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: 0.8512 (t0) cc_final: 0.7540 (t0) outliers start: 69 outliers final: 18 residues processed: 910 average time/residue: 0.1798 time to fit residues: 255.5292 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 : 0.932 ------------------------------------------------------------------------------- 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... 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 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 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 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.130960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.109898 restraints weight = 54521.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.111159 restraints weight = 47610.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.112250 restraints weight = 39665.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112677 restraints weight = 31666.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.112945 restraints weight = 29676.057| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.108 | | 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 = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26962 Z= 0.278 Angle : 1.036 13.321 36888 Z= 0.502 Chirality : 0.055 0.423 4503 Planarity : 0.008 0.144 4458 Dihedral : 7.693 46.918 3432 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.97 % Favored : 87.46 % Rotamer: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.49 % Twisted Proline : 2.27 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.13), residues: 3183 helix: -1.42 (0.24), residues: 387 sheet: -2.12 (0.15), residues: 1065 loop : -3.66 (0.11), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 273 TYR 0.030 0.003 TYR L 103 PHE 0.032 0.003 PHE P 63 TRP 0.039 0.003 TRP F 45 HIS 0.010 0.002 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.28 (26790) covalent geometry : angle 0.97690 / 0.49 (36429) SS BOND : bond 0.00569 / 0.39 ( 45) SS BOND : angle 1.88225 / 1.34 ( 90) hydrogen bonds : bond 0.04881 / 3.19 ( 779) hydrogen bonds : angle 7.13707 / 5.07 ( 2226) Misc. bond : bond 0.00944 / 0.50 ( 4) link_ALPHA1-2 : bond 0.00421 / 0.24 ( 9) link_ALPHA1-2 : angle 1.84948 / 1.35 ( 27) link_ALPHA1-3 : bond 0.00578 / 0.38 ( 12) link_ALPHA1-3 : angle 2.27733 / 1.52 ( 36) link_ALPHA1-6 : bond 0.00209 / 0.14 ( 9) link_ALPHA1-6 : angle 1.89667 / 1.39 ( 27) link_BETA1-4 : bond 0.00984 / 0.54 ( 39) link_BETA1-4 : angle 2.48444 / 1.75 ( 117) link_NAG-ASN : bond 0.00925 / 0.59 ( 54) link_NAG-ASN : angle 4.56574 / 3.40 ( 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 603 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 598 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8380 (tp30) REVERT: A 629 MET cc_start: 0.7260 (mmt) cc_final: 0.6911 (mmp) REVERT: A 643 TYR cc_start: 0.8028 (m-80) cc_final: 0.7661 (m-80) REVERT: B 530 MET cc_start: 0.7235 (mtp) cc_final: 0.6522 (mtp) REVERT: B 620 ASN cc_start: 0.7792 (t0) cc_final: 0.7553 (p0) REVERT: B 629 MET cc_start: 0.7170 (mmt) cc_final: 0.6307 (mmp) REVERT: C 565 MET cc_start: 0.5449 (mmm) cc_final: 0.5235 (mmp) REVERT: C 589 ASP cc_start: 0.9124 (m-30) cc_final: 0.8555 (m-30) REVERT: C 629 MET cc_start: 0.7070 (mmt) cc_final: 0.6301 (mmp) REVERT: D 40 TYR cc_start: 0.8592 (t80) cc_final: 0.8362 (t80) REVERT: D 95 MET cc_start: 0.7543 (ttp) cc_final: 0.6902 (ttp) REVERT: D 423 ILE cc_start: 0.8490 (mt) cc_final: 0.7846 (mt) REVERT: D 477 ASP cc_start: 0.7478 (t0) cc_final: 0.7259 (t0) REVERT: E 95 MET cc_start: 0.7784 (ttp) cc_final: 0.6863 (ttp) REVERT: E 160 ASN cc_start: 0.7875 (p0) cc_final: 0.7641 (p0) REVERT: E 353 PHE cc_start: 0.7772 (m-10) cc_final: 0.7547 (m-80) REVERT: E 426 MET cc_start: 0.8465 (mtp) cc_final: 0.8189 (mtp) REVERT: E 475 MET cc_start: 0.7762 (mmt) cc_final: 0.7232 (tpp) REVERT: E 477 ASP cc_start: 0.7615 (t70) cc_final: 0.7345 (t0) REVERT: F 40 TYR cc_start: 0.8592 (t80) cc_final: 0.8369 (t80) REVERT: F 423 ILE cc_start: 0.8769 (mt) cc_final: 0.8396 (mt) REVERT: F 475 MET cc_start: 0.8664 (mmp) cc_final: 0.7784 (mmm) REVERT: G 5 LEU cc_start: 0.8233 (mp) cc_final: 0.7872 (tt) REVERT: G 16 CYS cc_start: 0.4534 (m) cc_final: 0.3832 (m) REVERT: H 5 LEU cc_start: 0.7866 (mp) cc_final: 0.7257 (tt) REVERT: H 78 ASP cc_start: 0.8251 (m-30) cc_final: 0.7955 (m-30) REVERT: H 79 SER cc_start: 0.8407 (m) cc_final: 0.7654 (p) REVERT: I 5 LEU cc_start: 0.7789 (mp) cc_final: 0.7389 (tt) REVERT: I 58 ARG cc_start: 0.7639 (ptm-80) cc_final: 0.7379 (ptm-80) REVERT: I 79 SER cc_start: 0.8486 (m) cc_final: 0.7894 (p) REVERT: J 10 GLU cc_start: 0.7317 (tp30) cc_final: 0.6290 (tp30) REVERT: J 76 THR cc_start: 0.8167 (p) cc_final: 0.7874 (p) REVERT: J 81 MET cc_start: 0.7945 (tmm) cc_final: 0.7641 (tmm) REVERT: J 95 TYR cc_start: 0.7832 (m-80) cc_final: 0.7342 (m-80) REVERT: L 12 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7997 (mmt180) REVERT: L 55 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6867 (mm-30) REVERT: L 76 THR cc_start: 0.7920 (p) cc_final: 0.7350 (p) REVERT: L 78 THR cc_start: 0.7756 (p) cc_final: 0.6835 (p) REVERT: L 88 SER cc_start: 0.6743 (m) cc_final: 0.6384 (t) REVERT: L 112 LEU cc_start: 0.8457 (mt) cc_final: 0.8194 (mp) REVERT: N 10 GLU cc_start: 0.7277 (tp30) cc_final: 0.7063 (tp30) REVERT: N 95 TYR cc_start: 0.7547 (m-80) cc_final: 0.7315 (m-80) REVERT: O 93 TRP cc_start: 0.8090 (t-100) cc_final: 0.7749 (t-100) REVERT: Q 2 ILE cc_start: 0.8889 (mt) cc_final: 0.8634 (mm) REVERT: Q 78 ASN cc_start: 0.8860 (t0) cc_final: 0.7656 (t0) REVERT: R 1 GLN cc_start: 0.7753 (pm20) cc_final: 0.7546 (pm20) REVERT: R 105 TYR cc_start: 0.8282 (t80) cc_final: 0.7899 (t80) REVERT: R 122 TRP cc_start: 0.8426 (m100) cc_final: 0.8027 (m100) REVERT: S 9 SER cc_start: 0.7530 (m) cc_final: 0.7271 (t) REVERT: S 78 ASN cc_start: 0.8355 (t0) cc_final: 0.7906 (t0) REVERT: S 101 GLN cc_start: 0.7403 (mt0) cc_final: 0.7001 (mp10) REVERT: T 105 TYR cc_start: 0.8329 (t80) cc_final: 0.7930 (t80) REVERT: U 78 ASN cc_start: 0.8564 (t0) cc_final: 0.7461 (t0) REVERT: U 101 GLN cc_start: 0.7051 (mt0) cc_final: 0.6772 (mp10) outliers start: 5 outliers final: 0 residues processed: 602 average time/residue: 0.1717 time to fit residues: 165.8536 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 : 0.981 ------------------------------------------------------------------------------- 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: 0.9980 chunk 284 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 239 optimal weight: 0.0040 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 344 GLN ** 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 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 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102496 restraints weight = 49942.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.104738 restraints weight = 30970.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105776 restraints weight = 23260.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106319 restraints weight = 18921.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106673 restraints weight = 16990.716| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26962 Z= 0.163 Angle : 0.866 13.871 36888 Z= 0.426 Chirality : 0.051 0.518 4503 Planarity : 0.006 0.112 4458 Dihedral : 6.995 46.164 3432 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.08 % Favored : 89.48 % Rotamer: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % 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 are not related in a simple way. whole: -3.79 (0.13), residues: 3183 helix: -1.03 (0.26), residues: 387 sheet: -1.64 (0.15), residues: 993 loop : -3.54 (0.11), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 273 TYR 0.022 0.002 TYR D 217 PHE 0.035 0.002 PHE T 63 TRP 0.028 0.002 TRP F 479 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (26790) covalent geometry : angle 0.80763 / 0.41 (36429) SS BOND : bond 0.00517 / 0.33 ( 45) SS BOND : angle 1.94655 / 1.32 ( 90) hydrogen bonds : bond 0.04096 / 2.71 ( 779) hydrogen bonds : angle 6.60433 / 4.70 ( 2226) Misc. bond : bond 0.00095 / 0.05 ( 4) link_ALPHA1-2 : bond 0.00358 / 0.21 ( 9) link_ALPHA1-2 : angle 1.57714 / 1.13 ( 27) link_ALPHA1-3 : bond 0.00696 / 0.45 ( 12) link_ALPHA1-3 : angle 1.61499 / 1.09 ( 36) link_ALPHA1-6 : bond 0.00256 / 0.14 ( 9) link_ALPHA1-6 : angle 1.69794 / 1.19 ( 27) link_BETA1-4 : bond 0.00944 / 0.48 ( 39) link_BETA1-4 : angle 2.19152 / 1.52 ( 117) link_NAG-ASN : bond 0.00900 / 0.59 ( 54) link_NAG-ASN : angle 4.13933 / 3.09 ( 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 606 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 601 time to evaluate : 1.036 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 591 GLN cc_start: 0.8450 (pm20) cc_final: 0.8069 (pm20) REVERT: A 643 TYR cc_start: 0.7921 (m-10) cc_final: 0.7700 (m-80) REVERT: B 589 ASP cc_start: 0.8878 (m-30) cc_final: 0.7875 (m-30) REVERT: B 620 ASN cc_start: 0.7911 (t0) cc_final: 0.7588 (p0) REVERT: B 629 MET cc_start: 0.7377 (mmt) cc_final: 0.6420 (mmp) REVERT: B 631 TRP cc_start: 0.5829 (m-90) cc_final: 0.4794 (m-10) REVERT: C 589 ASP cc_start: 0.9178 (m-30) cc_final: 0.8447 (m-30) REVERT: C 620 ASN cc_start: 0.7783 (t0) cc_final: 0.7369 (p0) REVERT: C 629 MET cc_start: 0.6850 (mmt) cc_final: 0.6185 (mmp) REVERT: D 95 MET cc_start: 0.7866 (ttp) cc_final: 0.7145 (ttp) REVERT: D 423 ILE cc_start: 0.8544 (mt) cc_final: 0.7955 (mt) REVERT: E 95 MET cc_start: 0.7753 (ttp) cc_final: 0.7072 (ttp) REVERT: E 160 ASN cc_start: 0.8081 (p0) cc_final: 0.7728 (p0) REVERT: E 194 ILE cc_start: 0.8450 (mm) cc_final: 0.8110 (tt) REVERT: E 477 ASP cc_start: 0.7611 (t70) cc_final: 0.7364 (t0) REVERT: F 95 MET cc_start: 0.7169 (mtm) cc_final: 0.6512 (mtp) REVERT: F 327 ARG cc_start: 0.6810 (mtt90) cc_final: 0.6379 (mtm180) REVERT: F 423 ILE cc_start: 0.8853 (mt) cc_final: 0.8532 (mt) REVERT: F 426 MET cc_start: 0.7981 (mtp) cc_final: 0.7546 (mtp) REVERT: F 463 ASN cc_start: 0.7906 (p0) cc_final: 0.7692 (p0) REVERT: F 475 MET cc_start: 0.8632 (mmp) cc_final: 0.8032 (mmm) REVERT: G 5 LEU cc_start: 0.8132 (mp) cc_final: 0.7877 (tt) REVERT: G 96 LEU cc_start: 0.7764 (mt) cc_final: 0.7521 (mt) REVERT: H 5 LEU cc_start: 0.7808 (mp) cc_final: 0.7399 (tt) REVERT: H 78 ASP cc_start: 0.8091 (m-30) cc_final: 0.7796 (m-30) REVERT: H 79 SER cc_start: 0.8350 (m) cc_final: 0.7605 (p) REVERT: I 5 LEU cc_start: 0.7822 (mp) cc_final: 0.7465 (tt) REVERT: I 79 SER cc_start: 0.8319 (m) cc_final: 0.7863 (p) REVERT: J 46 GLU cc_start: 0.8972 (tp30) cc_final: 0.8727 (tp30) REVERT: J 76 THR cc_start: 0.8144 (p) cc_final: 0.7796 (p) REVERT: J 95 TYR cc_start: 0.7827 (m-80) cc_final: 0.7473 (m-80) REVERT: J 107 THR cc_start: 0.6317 (m) cc_final: 0.5674 (m) REVERT: K 108 LYS cc_start: 0.8442 (pttp) cc_final: 0.8237 (mmtm) REVERT: K 109 LEU cc_start: 0.8181 (tp) cc_final: 0.7979 (tp) REVERT: L 12 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7989 (mmt180) REVERT: L 55 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6700 (mm-30) REVERT: L 76 THR cc_start: 0.7878 (p) cc_final: 0.7398 (p) REVERT: L 80 TYR cc_start: 0.6778 (m-80) cc_final: 0.6499 (m-10) REVERT: M 88 TYR cc_start: 0.7525 (m-10) cc_final: 0.7294 (m-10) REVERT: M 93 TRP cc_start: 0.7939 (t-100) cc_final: 0.7283 (t-100) REVERT: M 101 GLN cc_start: 0.8794 (tt0) cc_final: 0.8396 (tt0) REVERT: N 46 GLU cc_start: 0.9009 (tp30) cc_final: 0.8587 (tp30) REVERT: N 78 THR cc_start: 0.7838 (p) cc_final: 0.7289 (p) REVERT: N 95 TYR cc_start: 0.7665 (m-80) cc_final: 0.7330 (m-80) REVERT: O 32 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7972 (ttpp) REVERT: O 48 LEU cc_start: 0.7360 (pt) cc_final: 0.6869 (pt) REVERT: O 50 ILE cc_start: 0.7123 (mt) cc_final: 0.6903 (mt) REVERT: O 99 THR cc_start: 0.7937 (p) cc_final: 0.7428 (p) REVERT: Q 70 THR cc_start: 0.7334 (p) cc_final: 0.6840 (p) REVERT: Q 78 ASN cc_start: 0.8786 (t0) cc_final: 0.7761 (t0) REVERT: R 1 GLN cc_start: 0.7766 (pm20) cc_final: 0.7535 (pm20) REVERT: R 122 TRP cc_start: 0.8452 (m100) cc_final: 0.8000 (m-10) REVERT: S 9 SER cc_start: 0.7521 (m) cc_final: 0.7221 (t) REVERT: S 78 ASN cc_start: 0.8464 (t0) cc_final: 0.7340 (t0) REVERT: T 111 LEU cc_start: 0.9229 (mm) cc_final: 0.8796 (mt) REVERT: T 122 TRP cc_start: 0.8767 (m100) cc_final: 0.7879 (m100) REVERT: T 124 GLN cc_start: 0.7293 (pp30) cc_final: 0.7029 (pp30) REVERT: U 23 CYS cc_start: 0.3167 (p) cc_final: 0.2268 (p) REVERT: U 27 GLN cc_start: 0.7967 (mp10) cc_final: 0.7703 (mp10) REVERT: U 36 TRP cc_start: 0.6786 (m100) cc_final: 0.6577 (m100) REVERT: U 78 ASN cc_start: 0.8588 (t0) cc_final: 0.8222 (t0) outliers start: 5 outliers final: 0 residues processed: 606 average time/residue: 0.1622 time to fit residues: 161.5978 Evaluate side-chains 413 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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: 2.9990 chunk 168 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 76 optimal weight: 0.4980 chunk 293 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 73 ASN I 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN K 33 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN M 7 GLN M 33 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN S 32 ASN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.123248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099432 restraints weight = 49974.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102556 restraints weight = 35042.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103646 restraints weight = 24392.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104032 restraints weight = 18470.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104276 restraints weight = 17016.913| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 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 = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26962 Z= 0.200 Angle : 0.876 13.419 36888 Z= 0.429 Chirality : 0.051 0.359 4503 Planarity : 0.006 0.122 4458 Dihedral : 6.763 44.286 3432 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.25 % Favored : 87.28 % Rotamer: Outliers : 0.15 % Allowed : 4.63 % Favored : 95.22 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -3.61 (0.13), residues: 3183 helix: -0.84 (0.26), residues: 387 sheet: -1.46 (0.15), residues: 1020 loop : -3.50 (0.11), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 273 TYR 0.024 0.002 TYR D 484 PHE 0.031 0.002 PHE T 63 TRP 0.033 0.002 TRP C 631 HIS 0.007 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (26790) covalent geometry : angle 0.82691 / 0.42 (36429) SS BOND : bond 0.00542 / 0.36 ( 45) SS BOND : angle 1.94583 / 1.37 ( 90) hydrogen bonds : bond 0.04038 / 2.64 ( 779) hydrogen bonds : angle 6.29239 / 4.45 ( 2226) Misc. bond : bond 0.00036 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00327 / 0.18 ( 9) link_ALPHA1-2 : angle 1.69888 / 1.24 ( 27) link_ALPHA1-3 : bond 0.00573 / 0.37 ( 12) link_ALPHA1-3 : angle 1.79332 / 1.21 ( 36) link_ALPHA1-6 : bond 0.00201 / 0.13 ( 9) link_ALPHA1-6 : angle 1.75098 / 1.25 ( 27) link_BETA1-4 : bond 0.00860 / 0.45 ( 39) link_BETA1-4 : angle 2.16130 / 1.49 ( 117) link_NAG-ASN : bond 0.00803 / 0.54 ( 54) link_NAG-ASN : angle 3.71806 / 2.76 ( 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 559 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 555 time to evaluate : 1.011 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: A 629 MET cc_start: 0.6348 (mmp) cc_final: 0.6021 (mmp) REVERT: A 643 TYR cc_start: 0.7798 (m-10) cc_final: 0.7548 (m-80) REVERT: B 620 ASN cc_start: 0.7838 (t0) cc_final: 0.7550 (p0) REVERT: C 589 ASP cc_start: 0.9125 (m-30) cc_final: 0.8409 (m-30) REVERT: C 620 ASN cc_start: 0.7804 (t0) cc_final: 0.7444 (p0) REVERT: C 629 MET cc_start: 0.7079 (mmt) cc_final: 0.6354 (mmp) REVERT: D 95 MET cc_start: 0.7937 (ttp) cc_final: 0.7075 (ttp) REVERT: D 104 MET cc_start: 0.8721 (tpp) cc_final: 0.8400 (tpt) REVERT: D 217 TYR cc_start: 0.7061 (m-80) cc_final: 0.6673 (m-80) REVERT: D 423 ILE cc_start: 0.8572 (mt) cc_final: 0.8066 (mt) REVERT: D 463 ASN cc_start: 0.8079 (p0) cc_final: 0.7815 (p0) REVERT: E 95 MET cc_start: 0.7915 (ttp) cc_final: 0.7242 (ttp) REVERT: E 106 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7728 (tm-30) REVERT: E 160 ASN cc_start: 0.7995 (p0) cc_final: 0.7755 (p0) REVERT: E 477 ASP cc_start: 0.7874 (t70) cc_final: 0.7554 (t0) REVERT: F 104 MET cc_start: 0.8231 (tpp) cc_final: 0.7844 (tpt) REVERT: F 423 ILE cc_start: 0.8847 (mt) cc_final: 0.8598 (mt) REVERT: G 5 LEU cc_start: 0.8016 (mp) cc_final: 0.7738 (tt) REVERT: G 96 LEU cc_start: 0.7742 (mt) cc_final: 0.7487 (mt) REVERT: H 5 LEU cc_start: 0.7782 (mp) cc_final: 0.7324 (tt) REVERT: H 78 ASP cc_start: 0.8124 (m-30) cc_final: 0.7879 (m-30) REVERT: H 79 SER cc_start: 0.8404 (m) cc_final: 0.7617 (p) REVERT: I 5 LEU cc_start: 0.7714 (mp) cc_final: 0.7361 (tt) REVERT: I 79 SER cc_start: 0.8313 (m) cc_final: 0.7796 (p) REVERT: J 46 GLU cc_start: 0.8938 (tp30) cc_final: 0.8683 (tp30) REVERT: J 81 MET cc_start: 0.7956 (tmm) cc_final: 0.7704 (tmm) REVERT: J 95 TYR cc_start: 0.7728 (m-80) cc_final: 0.7409 (m-80) REVERT: K 108 LYS cc_start: 0.8439 (pttp) cc_final: 0.8179 (mmtm) REVERT: L 12 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8054 (mmt180) REVERT: L 55 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6804 (mm-30) REVERT: L 76 THR cc_start: 0.7959 (p) cc_final: 0.7746 (p) REVERT: L 78 THR cc_start: 0.7739 (p) cc_final: 0.7534 (p) REVERT: L 80 TYR cc_start: 0.6708 (m-80) cc_final: 0.6494 (m-10) REVERT: L 87 ARG cc_start: 0.8377 (mmt90) cc_final: 0.8150 (mmt90) REVERT: L 107 THR cc_start: 0.6873 (m) cc_final: 0.6653 (p) REVERT: M 32 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7818 (ttpp) REVERT: M 93 TRP cc_start: 0.7969 (t-100) cc_final: 0.7472 (t-100) REVERT: M 101 GLN cc_start: 0.8550 (tt0) cc_final: 0.8183 (tt0) REVERT: N 46 GLU cc_start: 0.8786 (tp30) cc_final: 0.8541 (tp30) REVERT: N 78 THR cc_start: 0.7863 (p) cc_final: 0.7303 (p) REVERT: O 32 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7799 (ttpp) REVERT: O 50 ILE cc_start: 0.7203 (mt) cc_final: 0.6939 (mt) REVERT: Q 2 ILE cc_start: 0.9312 (mm) cc_final: 0.9072 (mm) REVERT: Q 70 THR cc_start: 0.7372 (p) cc_final: 0.6936 (p) REVERT: Q 78 ASN cc_start: 0.8706 (t0) cc_final: 0.7549 (t0) REVERT: R 100 THR cc_start: 0.8757 (p) cc_final: 0.8556 (p) REVERT: R 122 TRP cc_start: 0.8532 (m100) cc_final: 0.8045 (m-10) REVERT: R 124 GLN cc_start: 0.7487 (pp30) cc_final: 0.7209 (tm-30) REVERT: S 9 SER cc_start: 0.7525 (m) cc_final: 0.7308 (t) REVERT: S 24 ARG cc_start: 0.7186 (mtp85) cc_final: 0.6737 (mtp85) REVERT: S 78 ASN cc_start: 0.8495 (t0) cc_final: 0.8015 (t0) REVERT: T 111 LEU cc_start: 0.9218 (mm) cc_final: 0.8846 (mt) REVERT: T 122 TRP cc_start: 0.8797 (m100) cc_final: 0.8026 (m100) REVERT: T 124 GLN cc_start: 0.7600 (pp30) cc_final: 0.7254 (tm-30) REVERT: U 23 CYS cc_start: 0.2525 (p) cc_final: 0.2092 (p) REVERT: U 36 TRP cc_start: 0.7184 (m100) cc_final: 0.6708 (m100) REVERT: U 66 SER cc_start: 0.8822 (t) cc_final: 0.8285 (m) REVERT: U 70 THR cc_start: 0.7407 (p) cc_final: 0.6861 (p) REVERT: U 78 ASN cc_start: 0.8511 (t0) cc_final: 0.8101 (t0) outliers start: 4 outliers final: 1 residues processed: 559 average time/residue: 0.1682 time to fit residues: 152.9253 Evaluate side-chains 426 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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: 0.9990 chunk 94 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 236 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN B 625 ASN ** D 216 HIS ** 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 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 104 ASN O 7 GLN Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 90 GLN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN U 101 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.124920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101197 restraints weight = 49490.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104617 restraints weight = 32073.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105499 restraints weight = 22792.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105751 restraints weight = 18153.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106713 restraints weight = 17182.697| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4173 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= 0.164 Angle : 0.840 13.416 36888 Z= 0.409 Chirality : 0.050 0.349 4503 Planarity : 0.006 0.109 4458 Dihedral : 6.509 43.112 3432 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.30 % Favored : 89.32 % Rotamer: Outliers : 0.19 % Allowed : 2.16 % Favored : 97.65 % 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 are not related in a simple way. whole: -3.38 (0.13), residues: 3183 helix: -0.56 (0.26), residues: 387 sheet: -1.25 (0.16), residues: 1011 loop : -3.40 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 273 TYR 0.023 0.002 TYR N 114 PHE 0.035 0.002 PHE S 99 TRP 0.035 0.002 TRP F 479 HIS 0.006 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (26790) covalent geometry : angle 0.78097 / 0.40 (36429) SS BOND : bond 0.00546 / 0.38 ( 45) SS BOND : angle 1.77229 / 1.24 ( 90) hydrogen bonds : bond 0.03801 / 2.49 ( 779) hydrogen bonds : angle 6.07686 / 4.29 ( 2226) Misc. bond : bond 0.00021 / 0.01 ( 4) link_ALPHA1-2 : bond 0.00311 / 0.17 ( 9) link_ALPHA1-2 : angle 1.55110 / 1.11 ( 27) link_ALPHA1-3 : bond 0.00714 / 0.45 ( 12) link_ALPHA1-3 : angle 1.63106 / 1.11 ( 36) link_ALPHA1-6 : bond 0.00264 / 0.16 ( 9) link_ALPHA1-6 : angle 1.64718 / 1.17 ( 27) link_BETA1-4 : bond 0.00906 / 0.47 ( 39) link_BETA1-4 : angle 2.13086 / 1.50 ( 117) link_NAG-ASN : bond 0.00823 / 0.51 ( 54) link_NAG-ASN : angle 4.11024 / 3.04 ( 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 584 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 579 time to evaluate : 0.922 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: 0.8502 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: A 602 ILE cc_start: 0.8857 (pt) cc_final: 0.8634 (mt) REVERT: A 629 MET cc_start: 0.6215 (mmp) cc_final: 0.5739 (mmp) REVERT: B 620 ASN cc_start: 0.7807 (t0) cc_final: 0.7548 (p0) REVERT: B 629 MET cc_start: 0.7293 (mmt) cc_final: 0.6526 (mmp) REVERT: C 589 ASP cc_start: 0.9064 (m-30) cc_final: 0.8022 (m-30) REVERT: C 620 ASN cc_start: 0.7856 (t0) cc_final: 0.7540 (p0) REVERT: C 629 MET cc_start: 0.7423 (mmt) cc_final: 0.6783 (mmp) REVERT: D 95 MET cc_start: 0.7907 (ttp) cc_final: 0.7145 (ttp) REVERT: D 104 MET cc_start: 0.8699 (tpp) cc_final: 0.8316 (tpp) REVERT: D 107 ASP cc_start: 0.7744 (t70) cc_final: 0.7474 (t70) REVERT: D 423 ILE cc_start: 0.8546 (mt) cc_final: 0.7708 (mt) REVERT: D 463 ASN cc_start: 0.7961 (p0) cc_final: 0.7635 (p0) REVERT: E 95 MET cc_start: 0.7914 (ttp) cc_final: 0.7299 (ttp) REVERT: E 104 MET cc_start: 0.8486 (tpp) cc_final: 0.8141 (tpp) REVERT: E 106 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7742 (tm-30) REVERT: E 217 TYR cc_start: 0.7400 (m-10) cc_final: 0.6651 (m-10) REVERT: E 477 ASP cc_start: 0.7814 (t70) cc_final: 0.7540 (t0) REVERT: G 96 LEU cc_start: 0.7651 (mt) cc_final: 0.7378 (mt) REVERT: H 79 SER cc_start: 0.8398 (m) cc_final: 0.7585 (p) REVERT: I 79 SER cc_start: 0.8269 (m) cc_final: 0.7770 (p) REVERT: I 92 GLU cc_start: 0.7716 (tt0) cc_final: 0.7433 (tm-30) REVERT: J 10 GLU cc_start: 0.8389 (tp30) cc_final: 0.7766 (tp30) REVERT: J 12 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7307 (mmt90) REVERT: J 46 GLU cc_start: 0.8811 (tp30) cc_final: 0.8568 (tp30) REVERT: J 76 THR cc_start: 0.8109 (p) cc_final: 0.7795 (p) REVERT: K 93 TRP cc_start: 0.7667 (t-100) cc_final: 0.7382 (t-100) REVERT: K 108 LYS cc_start: 0.8362 (pttp) cc_final: 0.8150 (mmtm) REVERT: L 12 ARG cc_start: 0.8002 (mmt180) cc_final: 0.7801 (mmt180) REVERT: L 30 THR cc_start: 0.7189 (p) cc_final: 0.6939 (p) REVERT: L 55 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6730 (mm-30) REVERT: L 78 THR cc_start: 0.7614 (p) cc_final: 0.7232 (p) REVERT: L 81 MET cc_start: 0.7950 (tmm) cc_final: 0.7732 (tmm) REVERT: L 88 SER cc_start: 0.6364 (m) cc_final: 0.5956 (t) REVERT: L 107 THR cc_start: 0.6891 (m) cc_final: 0.6605 (m) REVERT: M 32 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7980 (ttpt) REVERT: M 93 TRP cc_start: 0.8046 (t-100) cc_final: 0.7573 (t60) REVERT: M 101 GLN cc_start: 0.8427 (tt0) cc_final: 0.8130 (tt0) REVERT: O 18 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7951 (ptmm) REVERT: O 50 ILE cc_start: 0.7057 (mt) cc_final: 0.6806 (mt) REVERT: O 99 THR cc_start: 0.7673 (p) cc_final: 0.7326 (p) REVERT: P 122 TRP cc_start: 0.8664 (m100) cc_final: 0.8312 (m100) REVERT: Q 2 ILE cc_start: 0.9257 (mm) cc_final: 0.9037 (mm) REVERT: Q 38 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7773 (tm-30) REVERT: Q 70 THR cc_start: 0.7196 (p) cc_final: 0.6726 (p) REVERT: Q 78 ASN cc_start: 0.8691 (t0) cc_final: 0.7525 (t0) REVERT: R 122 TRP cc_start: 0.8488 (m100) cc_final: 0.8065 (m-10) REVERT: S 24 ARG cc_start: 0.7135 (mtp85) cc_final: 0.6921 (mtp85) REVERT: S 66 SER cc_start: 0.8533 (t) cc_final: 0.8090 (m) REVERT: S 78 ASN cc_start: 0.8341 (t0) cc_final: 0.7287 (t0) REVERT: T 111 LEU cc_start: 0.9216 (mm) cc_final: 0.8857 (mt) REVERT: T 122 TRP cc_start: 0.8756 (m100) cc_final: 0.7872 (m100) REVERT: U 4 MET cc_start: 0.7476 (tpp) cc_final: 0.6651 (tpp) REVERT: U 23 CYS cc_start: 0.2474 (p) cc_final: 0.1796 (p) REVERT: U 36 TRP cc_start: 0.7250 (m100) cc_final: 0.6427 (m100) REVERT: U 66 SER cc_start: 0.8747 (t) cc_final: 0.8277 (m) REVERT: U 78 ASN cc_start: 0.8474 (t0) cc_final: 0.7438 (t0) outliers start: 5 outliers final: 0 residues processed: 582 average time/residue: 0.1604 time to fit residues: 152.8314 Evaluate side-chains 442 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 4.9990 chunk 187 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 126 optimal weight: 0.0770 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 216 HIS ** 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 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 ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN S 27 GLN S 32 ASN ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 101 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.121600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098173 restraints weight = 51127.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101713 restraints weight = 33501.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102368 restraints weight = 24846.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102701 restraints weight = 19164.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103781 restraints weight = 18090.880| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 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 = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (24 function evaluations) r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26962 Z= 0.200 Angle : 0.879 14.395 36888 Z= 0.427 Chirality : 0.051 0.346 4503 Planarity : 0.006 0.116 4458 Dihedral : 6.492 43.323 3432 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.88 % Favored : 87.72 % Rotamer: Outliers : 0.11 % Allowed : 1.86 % 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 are not related in a simple way. whole: -3.34 (0.13), residues: 3183 helix: -0.54 (0.26), residues: 387 sheet: -1.23 (0.16), residues: 1041 loop : -3.39 (0.12), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 273 TYR 0.027 0.002 TYR D 484 PHE 0.032 0.002 PHE T 63 TRP 0.032 0.002 TRP C 631 HIS 0.007 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (26790) covalent geometry : angle 0.81636 / 0.41 (36429) SS BOND : bond 0.00696 / 0.47 ( 45) SS BOND : angle 1.80970 / 1.29 ( 90) hydrogen bonds : bond 0.03973 / 2.61 ( 779) hydrogen bonds : angle 6.06929 / 4.27 ( 2226) Misc. bond : bond 0.00018 / 0.01 ( 4) link_ALPHA1-2 : bond 0.00314 / 0.16 ( 9) link_ALPHA1-2 : angle 1.69636 / 1.24 ( 27) link_ALPHA1-3 : bond 0.00568 / 0.37 ( 12) link_ALPHA1-3 : angle 1.75157 / 1.18 ( 36) link_ALPHA1-6 : bond 0.00217 / 0.15 ( 9) link_ALPHA1-6 : angle 1.74170 / 1.26 ( 27) link_BETA1-4 : bond 0.00881 / 0.47 ( 39) link_BETA1-4 : angle 2.13690 / 1.48 ( 117) link_NAG-ASN : bond 0.00788 / 0.52 ( 54) link_NAG-ASN : angle 4.39769 / 3.31 ( 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 559 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 556 time to evaluate : 0.917 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: A 585 ARG cc_start: 0.8086 (ttt180) cc_final: 0.7539 (ttt180) REVERT: A 629 MET cc_start: 0.6512 (mmp) cc_final: 0.6007 (mmp) REVERT: A 643 TYR cc_start: 0.7576 (m-80) cc_final: 0.7122 (m-80) REVERT: B 620 ASN cc_start: 0.8003 (t0) cc_final: 0.7651 (p0) REVERT: C 589 ASP cc_start: 0.9036 (m-30) cc_final: 0.7992 (m-30) REVERT: C 620 ASN cc_start: 0.7969 (t0) cc_final: 0.7552 (p0) REVERT: C 629 MET cc_start: 0.7643 (mmt) cc_final: 0.7144 (mmt) REVERT: D 95 MET cc_start: 0.7894 (ttp) cc_final: 0.6962 (ttp) REVERT: D 423 ILE cc_start: 0.8610 (mt) cc_final: 0.7909 (mt) REVERT: D 463 ASN cc_start: 0.8058 (p0) cc_final: 0.7758 (p0) REVERT: E 104 MET cc_start: 0.8488 (tpp) cc_final: 0.8151 (tpp) REVERT: E 106 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7722 (tm-30) REVERT: E 217 TYR cc_start: 0.7512 (m-10) cc_final: 0.6306 (m-80) REVERT: F 106 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7621 (tm-30) REVERT: H 79 SER cc_start: 0.8432 (m) cc_final: 0.7627 (p) REVERT: I 79 SER cc_start: 0.8238 (m) cc_final: 0.7725 (p) REVERT: J 10 GLU cc_start: 0.8390 (tp30) cc_final: 0.7677 (tp30) REVERT: J 12 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7196 (mmt90) REVERT: J 46 GLU cc_start: 0.8832 (tp30) cc_final: 0.8486 (tp30) REVERT: J 67 ARG cc_start: 0.3856 (ptt180) cc_final: 0.3518 (ptt180) REVERT: J 76 THR cc_start: 0.8097 (p) cc_final: 0.7602 (p) REVERT: J 78 THR cc_start: 0.8185 (p) cc_final: 0.7946 (p) REVERT: J 81 MET cc_start: 0.7939 (tmm) cc_final: 0.7708 (tmm) REVERT: K 18 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7897 (ptmm) REVERT: K 108 LYS cc_start: 0.8286 (pttp) cc_final: 0.8020 (mptt) REVERT: K 109 LEU cc_start: 0.7715 (tp) cc_final: 0.7472 (tp) REVERT: L 55 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6902 (mm-30) REVERT: L 76 THR cc_start: 0.8007 (p) cc_final: 0.7529 (p) REVERT: L 78 THR cc_start: 0.7885 (p) cc_final: 0.7311 (p) REVERT: L 81 MET cc_start: 0.7840 (tmm) cc_final: 0.7484 (tmm) REVERT: L 88 SER cc_start: 0.5954 (m) cc_final: 0.5438 (t) REVERT: L 107 THR cc_start: 0.6858 (m) cc_final: 0.6516 (m) REVERT: M 32 LYS cc_start: 0.8527 (ttmm) cc_final: 0.7969 (ttpp) REVERT: M 55 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8210 (mp10) REVERT: M 82 THR cc_start: 0.7158 (m) cc_final: 0.6804 (m) REVERT: M 101 GLN cc_start: 0.8460 (tt0) cc_final: 0.8047 (tt0) REVERT: O 50 ILE cc_start: 0.6901 (mt) cc_final: 0.6670 (mt) REVERT: O 108 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8029 (mptt) REVERT: P 122 TRP cc_start: 0.8719 (m100) cc_final: 0.8306 (m100) REVERT: Q 38 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7871 (tm-30) REVERT: Q 70 THR cc_start: 0.7105 (p) cc_final: 0.6802 (p) REVERT: Q 78 ASN cc_start: 0.8693 (t0) cc_final: 0.7575 (t0) REVERT: R 122 TRP cc_start: 0.8587 (m100) cc_final: 0.8222 (m-10) REVERT: S 24 ARG cc_start: 0.7179 (mtp85) cc_final: 0.6960 (mtp85) REVERT: S 66 SER cc_start: 0.8457 (t) cc_final: 0.8004 (m) REVERT: S 78 ASN cc_start: 0.8408 (t0) cc_final: 0.7911 (t0) REVERT: T 111 LEU cc_start: 0.9216 (mm) cc_final: 0.8828 (mt) REVERT: T 122 TRP cc_start: 0.8772 (m100) cc_final: 0.8108 (m100) REVERT: U 66 SER cc_start: 0.8800 (t) cc_final: 0.8322 (m) REVERT: U 78 ASN cc_start: 0.8505 (t0) cc_final: 0.8122 (t0) outliers start: 3 outliers final: 0 residues processed: 558 average time/residue: 0.1640 time to fit residues: 148.0943 Evaluate side-chains 435 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 6.9990 chunk 297 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 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 M 7 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN O 7 GLN O 33 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN S 101 GLN U 32 ASN U 101 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.121387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097671 restraints weight = 51032.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099306 restraints weight = 35332.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100756 restraints weight = 26415.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101161 restraints weight = 21036.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101454 restraints weight = 18922.331| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26962 Z= 0.199 Angle : 0.874 16.205 36888 Z= 0.426 Chirality : 0.051 0.356 4503 Planarity : 0.006 0.116 4458 Dihedral : 6.446 42.944 3432 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.28 % Favored : 88.31 % Rotamer: Outliers : 0.15 % Allowed : 1.52 % Favored : 98.33 % 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 are not related in a simple way. whole: -3.30 (0.13), residues: 3183 helix: -0.51 (0.26), residues: 387 sheet: -1.23 (0.16), residues: 1020 loop : -3.34 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 273 TYR 0.016 0.002 TYR Q 92 PHE 0.031 0.002 PHE T 63 TRP 0.019 0.002 TRP A 631 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (26790) covalent geometry : angle 0.81920 / 0.41 (36429) SS BOND : bond 0.00553 / 0.37 ( 45) SS BOND : angle 1.86578 / 1.30 ( 90) hydrogen bonds : bond 0.03925 / 2.57 ( 779) hydrogen bonds : angle 5.99894 / 4.22 ( 2226) Misc. bond : bond 0.00111 / 0.06 ( 4) link_ALPHA1-2 : bond 0.00309 / 0.16 ( 9) link_ALPHA1-2 : angle 1.66130 / 1.21 ( 27) link_ALPHA1-3 : bond 0.00578 / 0.38 ( 12) link_ALPHA1-3 : angle 1.69755 / 1.14 ( 36) link_ALPHA1-6 : bond 0.00238 / 0.16 ( 9) link_ALPHA1-6 : angle 1.73059 / 1.26 ( 27) link_BETA1-4 : bond 0.00839 / 0.44 ( 39) link_BETA1-4 : angle 2.12618 / 1.49 ( 117) link_NAG-ASN : bond 0.00756 / 0.49 ( 54) link_NAG-ASN : angle 4.04262 / 3.05 ( 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 549 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 545 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: A 591 GLN cc_start: 0.8479 (pm20) cc_final: 0.7946 (pm20) REVERT: A 629 MET cc_start: 0.6679 (mmp) cc_final: 0.6227 (mmp) REVERT: B 620 ASN cc_start: 0.8093 (t0) cc_final: 0.7591 (p0) REVERT: C 589 ASP cc_start: 0.9031 (m-30) cc_final: 0.7903 (m-30) REVERT: C 620 ASN cc_start: 0.8019 (t0) cc_final: 0.7622 (p0) REVERT: C 629 MET cc_start: 0.7659 (mmt) cc_final: 0.7101 (mmt) REVERT: D 95 MET cc_start: 0.7957 (ttp) cc_final: 0.6979 (ttp) REVERT: D 423 ILE cc_start: 0.8615 (mt) cc_final: 0.7793 (mt) REVERT: D 463 ASN cc_start: 0.8165 (p0) cc_final: 0.7828 (p0) REVERT: E 104 MET cc_start: 0.8514 (tpp) cc_final: 0.8281 (tpp) REVERT: E 106 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7722 (tm-30) REVERT: F 104 MET cc_start: 0.8542 (tpp) cc_final: 0.8112 (tpp) REVERT: G 78 ASP cc_start: 0.8140 (m-30) cc_final: 0.7910 (m-30) REVERT: H 78 ASP cc_start: 0.8420 (m-30) cc_final: 0.8199 (m-30) REVERT: H 79 SER cc_start: 0.8442 (m) cc_final: 0.7655 (p) REVERT: I 79 SER cc_start: 0.8284 (m) cc_final: 0.7813 (p) REVERT: J 46 GLU cc_start: 0.8948 (tp30) cc_final: 0.8530 (tp30) REVERT: J 67 ARG cc_start: 0.3762 (ptt180) cc_final: 0.3447 (ptt180) REVERT: J 80 TYR cc_start: 0.6946 (m-10) cc_final: 0.6642 (m-10) REVERT: J 81 MET cc_start: 0.7745 (tmm) cc_final: 0.7474 (tmm) REVERT: K 93 TRP cc_start: 0.7923 (t-100) cc_final: 0.7692 (t-100) REVERT: K 108 LYS cc_start: 0.8374 (pttp) cc_final: 0.8043 (mmtm) REVERT: L 55 GLU cc_start: 0.7717 (mm-30) cc_final: 0.6984 (mm-30) REVERT: L 81 MET cc_start: 0.7750 (tmm) cc_final: 0.6948 (tmm) REVERT: L 107 THR cc_start: 0.7156 (m) cc_final: 0.6759 (m) REVERT: M 93 TRP cc_start: 0.8079 (t-100) cc_final: 0.7668 (t-100) REVERT: M 101 GLN cc_start: 0.8513 (tt0) cc_final: 0.8060 (tt0) REVERT: N 46 GLU cc_start: 0.8775 (tp30) cc_final: 0.8516 (tp30) REVERT: N 107 THR cc_start: 0.7069 (m) cc_final: 0.6761 (p) REVERT: O 18 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7989 (ptmm) REVERT: O 99 THR cc_start: 0.7422 (p) cc_final: 0.6905 (p) REVERT: O 108 LYS cc_start: 0.8472 (ptmt) cc_final: 0.8041 (mptt) REVERT: O 109 LEU cc_start: 0.7896 (tp) cc_final: 0.7605 (tp) REVERT: P 122 TRP cc_start: 0.8693 (m100) cc_final: 0.8272 (m100) REVERT: Q 66 SER cc_start: 0.8182 (t) cc_final: 0.7912 (m) REVERT: Q 70 THR cc_start: 0.7171 (p) cc_final: 0.6919 (p) REVERT: Q 78 ASN cc_start: 0.8721 (t0) cc_final: 0.7553 (t0) REVERT: R 1 GLN cc_start: 0.8014 (pm20) cc_final: 0.7410 (pm20) REVERT: R 122 TRP cc_start: 0.8529 (m100) cc_final: 0.8099 (m-10) REVERT: S 24 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6913 (mtp85) REVERT: S 66 SER cc_start: 0.8505 (t) cc_final: 0.8107 (m) REVERT: S 78 ASN cc_start: 0.8473 (t0) cc_final: 0.7451 (t0) REVERT: T 111 LEU cc_start: 0.9269 (mm) cc_final: 0.8902 (mt) REVERT: T 122 TRP cc_start: 0.8793 (m100) cc_final: 0.8125 (m100) REVERT: U 66 SER cc_start: 0.8659 (t) cc_final: 0.8193 (m) REVERT: U 78 ASN cc_start: 0.8528 (t0) cc_final: 0.7426 (t0) outliers start: 4 outliers final: 0 residues processed: 549 average time/residue: 0.1702 time to fit residues: 151.2383 Evaluate side-chains 428 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN D 99 ASN ** 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** O 7 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 GLN S 32 ASN S 90 GLN S 101 GLN U 6 GLN U 32 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.125019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101290 restraints weight = 50105.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103614 restraints weight = 32456.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104935 restraints weight = 25810.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.105051 restraints weight = 20547.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.106165 restraints weight = 18229.961| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26962 Z= 0.145 Angle : 0.822 13.382 36888 Z= 0.403 Chirality : 0.050 0.362 4503 Planarity : 0.005 0.089 4458 Dihedral : 6.130 40.086 3432 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.12 % Favored : 89.44 % Rotamer: Outliers : 0.19 % Allowed : 1.06 % Favored : 98.75 % 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 are not related in a simple way. whole: -3.13 (0.13), residues: 3183 helix: -0.21 (0.27), residues: 369 sheet: -1.07 (0.16), residues: 993 loop : -3.25 (0.12), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 63 TYR 0.029 0.002 TYR F 484 PHE 0.026 0.002 PHE J 51 TRP 0.028 0.002 TRP C 631 HIS 0.007 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (26790) covalent geometry : angle 0.76923 / 0.39 (36429) SS BOND : bond 0.00592 / 0.41 ( 45) SS BOND : angle 1.59519 / 1.13 ( 90) hydrogen bonds : bond 0.03626 / 2.39 ( 779) hydrogen bonds : angle 5.82214 / 4.10 ( 2226) Misc. bond : bond 0.00076 / 0.04 ( 4) link_ALPHA1-2 : bond 0.00311 / 0.18 ( 9) link_ALPHA1-2 : angle 1.50317 / 1.05 ( 27) link_ALPHA1-3 : bond 0.00645 / 0.41 ( 12) link_ALPHA1-3 : angle 1.48845 / 1.00 ( 36) link_ALPHA1-6 : bond 0.00315 / 0.19 ( 9) link_ALPHA1-6 : angle 1.57913 / 1.11 ( 27) link_BETA1-4 : bond 0.00896 / 0.46 ( 39) link_BETA1-4 : angle 1.92134 / 1.33 ( 117) link_NAG-ASN : bond 0.00719 / 0.46 ( 54) link_NAG-ASN : angle 3.94952 / 2.98 ( 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 567 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 562 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8805 (pp) cc_final: 0.8582 (pp) REVERT: A 587 LEU cc_start: 0.9037 (mm) cc_final: 0.8251 (mm) REVERT: A 591 GLN cc_start: 0.8518 (pm20) cc_final: 0.8040 (pm20) REVERT: A 618 THR cc_start: 0.8031 (p) cc_final: 0.7629 (p) REVERT: A 629 MET cc_start: 0.6586 (mmp) cc_final: 0.6168 (mmp) REVERT: B 590 GLN cc_start: 0.8883 (tp40) cc_final: 0.8552 (tp40) REVERT: B 620 ASN cc_start: 0.8124 (t0) cc_final: 0.7646 (p0) REVERT: C 523 LEU cc_start: 0.8717 (pt) cc_final: 0.8306 (pp) REVERT: C 530 MET cc_start: 0.6401 (mtt) cc_final: 0.5792 (mtt) REVERT: C 589 ASP cc_start: 0.8976 (m-30) cc_final: 0.7919 (m-30) REVERT: C 620 ASN cc_start: 0.8024 (t0) cc_final: 0.7630 (p0) REVERT: C 629 MET cc_start: 0.7587 (mmt) cc_final: 0.7101 (mmt) REVERT: D 95 MET cc_start: 0.7935 (ttp) cc_final: 0.7212 (ttp) REVERT: D 104 MET cc_start: 0.8740 (tpp) cc_final: 0.8233 (tpp) REVERT: D 423 ILE cc_start: 0.8530 (mt) cc_final: 0.7976 (mm) REVERT: D 463 ASN cc_start: 0.8082 (p0) cc_final: 0.7790 (p0) REVERT: E 95 MET cc_start: 0.7784 (ttp) cc_final: 0.7101 (ttp) REVERT: F 104 MET cc_start: 0.8362 (tpp) cc_final: 0.7936 (tpp) REVERT: G 79 SER cc_start: 0.8270 (m) cc_final: 0.7505 (p) REVERT: H 78 ASP cc_start: 0.8085 (m-30) cc_final: 0.7882 (m-30) REVERT: H 79 SER cc_start: 0.8434 (m) cc_final: 0.7628 (p) REVERT: I 79 SER cc_start: 0.8223 (m) cc_final: 0.7779 (p) REVERT: I 92 GLU cc_start: 0.7878 (tt0) cc_final: 0.7487 (tm-30) REVERT: J 46 GLU cc_start: 0.8872 (tp30) cc_final: 0.8436 (tp30) REVERT: J 67 ARG cc_start: 0.3572 (ptt180) cc_final: 0.3211 (ptt180) REVERT: J 80 TYR cc_start: 0.7017 (m-10) cc_final: 0.6659 (m-10) REVERT: J 90 ASP cc_start: 0.6055 (m-30) cc_final: 0.5759 (m-30) REVERT: K 55 GLN cc_start: 0.8180 (mp-120) cc_final: 0.7947 (mp10) REVERT: K 108 LYS cc_start: 0.8355 (pttp) cc_final: 0.8006 (mmtm) REVERT: L 55 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6980 (mm-30) REVERT: L 81 MET cc_start: 0.7530 (tmm) cc_final: 0.7222 (tmm) REVERT: L 85 SER cc_start: 0.7449 (t) cc_final: 0.7192 (p) REVERT: L 88 SER cc_start: 0.6176 (m) cc_final: 0.5774 (t) REVERT: L 90 ASP cc_start: 0.5749 (m-30) cc_final: 0.5297 (m-30) REVERT: L 107 THR cc_start: 0.7110 (m) cc_final: 0.6778 (m) REVERT: M 93 TRP cc_start: 0.7913 (t-100) cc_final: 0.7550 (t60) REVERT: M 101 GLN cc_start: 0.8428 (tt0) cc_final: 0.8041 (tt0) REVERT: N 46 GLU cc_start: 0.8706 (tp30) cc_final: 0.8495 (tp30) REVERT: N 76 THR cc_start: 0.8183 (p) cc_final: 0.7848 (p) REVERT: N 78 THR cc_start: 0.8270 (p) cc_final: 0.7928 (p) REVERT: O 99 THR cc_start: 0.7430 (p) cc_final: 0.7002 (p) REVERT: O 108 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8164 (mptt) REVERT: P 122 TRP cc_start: 0.8590 (m100) cc_final: 0.8172 (m100) REVERT: Q 2 ILE cc_start: 0.8946 (mm) cc_final: 0.8697 (mm) REVERT: Q 78 ASN cc_start: 0.8723 (t0) cc_final: 0.7537 (t0) REVERT: R 1 GLN cc_start: 0.7991 (pm20) cc_final: 0.7451 (pm20) REVERT: R 111 LEU cc_start: 0.9209 (mm) cc_final: 0.8514 (mt) REVERT: S 24 ARG cc_start: 0.7120 (mtp85) cc_final: 0.6777 (mtp85) REVERT: S 78 ASN cc_start: 0.8447 (t0) cc_final: 0.7378 (t0) REVERT: T 111 LEU cc_start: 0.9205 (mm) cc_final: 0.8651 (mt) REVERT: T 122 TRP cc_start: 0.8721 (m100) cc_final: 0.7944 (m100) REVERT: U 66 SER cc_start: 0.8690 (t) cc_final: 0.8369 (m) REVERT: U 78 ASN cc_start: 0.8533 (t0) cc_final: 0.7402 (t0) outliers start: 5 outliers final: 0 residues processed: 564 average time/residue: 0.1556 time to fit residues: 142.9156 Evaluate side-chains 424 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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: 0.0870 chunk 3 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 0.0670 chunk 94 optimal weight: 0.0770 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 185 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 99 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 GLN F 99 ASN G 73 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 124 GLN S 32 ASN S 101 GLN T 124 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.126905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103707 restraints weight = 49997.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104859 restraints weight = 31806.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106308 restraints weight = 25294.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.107189 restraints weight = 19476.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107386 restraints weight = 17491.608| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26962 Z= 0.138 Angle : 0.814 13.364 36888 Z= 0.400 Chirality : 0.050 0.359 4503 Planarity : 0.006 0.090 4458 Dihedral : 5.969 39.421 3432 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.52 % Favored : 90.07 % Rotamer: Outliers : 0.23 % Allowed : 0.87 % Favored : 98.90 % 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 are not related in a simple way. whole: -3.04 (0.13), residues: 3183 helix: -0.13 (0.27), residues: 369 sheet: -0.98 (0.16), residues: 996 loop : -3.21 (0.12), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 63 TYR 0.029 0.002 TYR D 484 PHE 0.038 0.002 PHE T 63 TRP 0.038 0.002 TRP O 93 HIS 0.007 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (26790) covalent geometry : angle 0.75999 / 0.39 (36429) SS BOND : bond 0.00467 / 0.32 ( 45) SS BOND : angle 1.45036 / 1.05 ( 90) hydrogen bonds : bond 0.03497 / 2.31 ( 779) hydrogen bonds : angle 5.72404 / 4.02 ( 2226) Misc. bond : bond 0.00053 / 0.03 ( 4) link_ALPHA1-2 : bond 0.00300 / 0.18 ( 9) link_ALPHA1-2 : angle 1.49338 / 1.03 ( 27) link_ALPHA1-3 : bond 0.00596 / 0.38 ( 12) link_ALPHA1-3 : angle 1.43629 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00310 / 0.18 ( 9) link_ALPHA1-6 : angle 1.54008 / 1.07 ( 27) link_BETA1-4 : bond 0.00876 / 0.45 ( 39) link_BETA1-4 : angle 1.88150 / 1.31 ( 117) link_NAG-ASN : bond 0.00659 / 0.42 ( 54) link_NAG-ASN : angle 4.01949 / 2.97 ( 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 565 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 559 time to evaluate : 0.993 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 587 LEU cc_start: 0.9039 (mm) cc_final: 0.8831 (mt) REVERT: A 629 MET cc_start: 0.6184 (mmp) cc_final: 0.5825 (mmp) REVERT: B 620 ASN cc_start: 0.8070 (t0) cc_final: 0.7571 (p0) REVERT: B 629 MET cc_start: 0.6162 (mmp) cc_final: 0.4698 (tpp) REVERT: C 523 LEU cc_start: 0.8687 (pt) cc_final: 0.8276 (pp) REVERT: C 589 ASP cc_start: 0.8937 (m-30) cc_final: 0.7878 (m-30) REVERT: C 618 THR cc_start: 0.7895 (p) cc_final: 0.7693 (p) REVERT: C 620 ASN cc_start: 0.8030 (t0) cc_final: 0.7606 (p0) REVERT: C 629 MET cc_start: 0.7503 (mmt) cc_final: 0.7065 (mmt) REVERT: C 643 TYR cc_start: 0.7732 (m-80) cc_final: 0.7408 (m-80) REVERT: D 95 MET cc_start: 0.7906 (ttp) cc_final: 0.7311 (ttp) REVERT: D 100 MET cc_start: 0.8431 (mtp) cc_final: 0.8177 (mtp) REVERT: D 423 ILE cc_start: 0.8517 (mt) cc_final: 0.7974 (mm) REVERT: D 463 ASN cc_start: 0.8111 (p0) cc_final: 0.7736 (p0) REVERT: E 95 MET cc_start: 0.7507 (ttp) cc_final: 0.7185 (ttp) REVERT: E 104 MET cc_start: 0.8570 (tpp) cc_final: 0.8207 (tpp) REVERT: F 104 MET cc_start: 0.8374 (tpp) cc_final: 0.7962 (tpp) REVERT: G 79 SER cc_start: 0.8249 (m) cc_final: 0.7523 (p) REVERT: H 78 ASP cc_start: 0.8024 (m-30) cc_final: 0.7815 (m-30) REVERT: H 79 SER cc_start: 0.8424 (m) cc_final: 0.7633 (p) REVERT: I 79 SER cc_start: 0.8290 (m) cc_final: 0.7795 (p) REVERT: I 92 GLU cc_start: 0.7826 (tt0) cc_final: 0.7448 (tm-30) REVERT: J 10 GLU cc_start: 0.8391 (tp30) cc_final: 0.7844 (tp30) REVERT: J 46 GLU cc_start: 0.8743 (tp30) cc_final: 0.8416 (tp30) REVERT: J 67 ARG cc_start: 0.3859 (ptt180) cc_final: 0.3539 (ptt180) REVERT: J 80 TYR cc_start: 0.6823 (m-10) cc_final: 0.6563 (m-10) REVERT: J 90 ASP cc_start: 0.5982 (m-30) cc_final: 0.5775 (m-30) REVERT: K 32 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7785 (ttpp) REVERT: K 108 LYS cc_start: 0.8310 (pttp) cc_final: 0.8025 (mmtm) REVERT: K 109 LEU cc_start: 0.7769 (tp) cc_final: 0.7569 (tp) REVERT: L 55 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7116 (mm-30) REVERT: L 72 GLU cc_start: 0.7319 (tp30) cc_final: 0.6953 (mp0) REVERT: L 90 ASP cc_start: 0.5714 (m-30) cc_final: 0.5311 (m-30) REVERT: L 107 THR cc_start: 0.7141 (m) cc_final: 0.6760 (m) REVERT: M 93 TRP cc_start: 0.7960 (t-100) cc_final: 0.7585 (t60) REVERT: N 67 ARG cc_start: 0.3903 (ptt180) cc_final: 0.3608 (ptt-90) REVERT: O 93 TRP cc_start: 0.7623 (t-100) cc_final: 0.7200 (t-100) REVERT: O 99 THR cc_start: 0.7270 (p) cc_final: 0.6825 (p) REVERT: O 108 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8201 (mptt) REVERT: P 122 TRP cc_start: 0.8705 (m100) cc_final: 0.8326 (m100) REVERT: Q 2 ILE cc_start: 0.8855 (mm) cc_final: 0.8515 (mm) REVERT: Q 78 ASN cc_start: 0.8712 (t0) cc_final: 0.7933 (t0) REVERT: R 1 GLN cc_start: 0.8014 (pm20) cc_final: 0.7489 (pm20) REVERT: R 111 LEU cc_start: 0.9204 (mm) cc_final: 0.8482 (mt) REVERT: S 78 ASN cc_start: 0.8400 (t0) cc_final: 0.7350 (t0) REVERT: T 111 LEU cc_start: 0.9196 (mm) cc_final: 0.8788 (mt) REVERT: T 122 TRP cc_start: 0.8696 (m100) cc_final: 0.8150 (m100) REVERT: U 66 SER cc_start: 0.8754 (t) cc_final: 0.8476 (m) REVERT: U 78 ASN cc_start: 0.8503 (t0) cc_final: 0.8091 (t0) outliers start: 6 outliers final: 0 residues processed: 561 average time/residue: 0.1582 time to fit residues: 144.6008 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 : 0.977 ------------------------------------------------------------------------------- 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: 7.9990 chunk 257 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN B 590 GLN D 99 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN D 330 HIS E 99 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 GLN F 99 ASN F 287 GLN F 330 HIS G 73 ASN G 94 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 56 ASN M 7 GLN ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN N 101 ASN O 7 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.118978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094961 restraints weight = 51957.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098045 restraints weight = 35512.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098386 restraints weight = 24950.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100354 restraints weight = 21630.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100334 restraints weight = 18085.415| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 26962 Z= 0.264 Angle : 0.954 12.869 36888 Z= 0.464 Chirality : 0.053 0.346 4503 Planarity : 0.006 0.129 4458 Dihedral : 6.494 42.199 3432 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.82 % Favored : 86.77 % Rotamer: Outliers : 0.15 % Allowed : 0.57 % Favored : 99.28 % 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 are not related in a simple way. whole: -3.20 (0.13), residues: 3183 helix: -0.24 (0.26), residues: 369 sheet: -1.12 (0.16), residues: 1038 loop : -3.33 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 273 TYR 0.039 0.002 TYR F 484 PHE 0.046 0.003 PHE F 382 TRP 0.041 0.003 TRP R 122 HIS 0.016 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (26790) covalent geometry : angle 0.89719 / 0.45 (36429) SS BOND : bond 0.00641 / 0.42 ( 45) SS BOND : angle 1.88570 / 1.32 ( 90) hydrogen bonds : bond 0.04292 / 2.79 ( 779) hydrogen bonds : angle 6.04044 / 4.24 ( 2226) Misc. bond : bond 0.00026 / 0.01 ( 4) link_ALPHA1-2 : bond 0.00349 / 0.20 ( 9) link_ALPHA1-2 : angle 1.90112 / 1.41 ( 27) link_ALPHA1-3 : bond 0.00519 / 0.34 ( 12) link_ALPHA1-3 : angle 1.92759 / 1.28 ( 36) link_ALPHA1-6 : bond 0.00200 / 0.15 ( 9) link_ALPHA1-6 : angle 1.81764 / 1.32 ( 27) link_BETA1-4 : bond 0.00896 / 0.50 ( 39) link_BETA1-4 : angle 2.21899 / 1.55 ( 117) link_NAG-ASN : bond 0.00829 / 0.55 ( 54) link_NAG-ASN : angle 4.31557 / 3.21 ( 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 524 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 520 time to evaluate : 1.047 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 587 LEU cc_start: 0.9133 (mm) cc_final: 0.8904 (mm) REVERT: A 618 THR cc_start: 0.8063 (p) cc_final: 0.7735 (p) REVERT: A 629 MET cc_start: 0.6998 (mmp) cc_final: 0.6608 (mmp) REVERT: B 620 ASN cc_start: 0.8170 (t0) cc_final: 0.7761 (p0) REVERT: C 530 MET cc_start: 0.7337 (mtt) cc_final: 0.6121 (mtt) REVERT: C 589 ASP cc_start: 0.9078 (m-30) cc_final: 0.8007 (m-30) REVERT: C 620 ASN cc_start: 0.7984 (t0) cc_final: 0.7635 (p0) REVERT: C 629 MET cc_start: 0.7848 (mmt) cc_final: 0.7302 (mmt) REVERT: C 643 TYR cc_start: 0.7949 (m-80) cc_final: 0.7555 (m-80) REVERT: D 95 MET cc_start: 0.8008 (ttp) cc_final: 0.7608 (ttp) REVERT: D 346 VAL cc_start: 0.8317 (t) cc_final: 0.8098 (p) REVERT: D 423 ILE cc_start: 0.8597 (mt) cc_final: 0.8134 (mt) REVERT: D 463 ASN cc_start: 0.8063 (p0) cc_final: 0.7768 (p0) REVERT: D 465 THR cc_start: 0.7326 (p) cc_final: 0.6820 (p) REVERT: E 104 MET cc_start: 0.8736 (tpp) cc_final: 0.8257 (tpp) REVERT: F 104 MET cc_start: 0.8611 (tpp) cc_final: 0.8362 (tpp) REVERT: F 475 MET cc_start: 0.8394 (mmm) cc_final: 0.8040 (tpp) REVERT: H 79 SER cc_start: 0.8408 (m) cc_final: 0.7622 (p) REVERT: I 79 SER cc_start: 0.8571 (m) cc_final: 0.7845 (p) REVERT: J 10 GLU cc_start: 0.8441 (tp30) cc_final: 0.8212 (tp30) REVERT: J 46 GLU cc_start: 0.8896 (tp30) cc_final: 0.8496 (tp30) REVERT: J 67 ARG cc_start: 0.4338 (ptt180) cc_final: 0.4090 (ptt180) REVERT: J 78 THR cc_start: 0.8645 (p) cc_final: 0.8286 (p) REVERT: J 80 TYR cc_start: 0.6861 (m-10) cc_final: 0.6398 (m-10) REVERT: L 10 GLU cc_start: 0.8457 (tp30) cc_final: 0.7955 (tp30) REVERT: L 55 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7116 (mm-30) REVERT: L 90 ASP cc_start: 0.5788 (m-30) cc_final: 0.5410 (m-30) REVERT: L 107 THR cc_start: 0.7098 (m) cc_final: 0.6826 (m) REVERT: N 10 GLU cc_start: 0.7928 (tp30) cc_final: 0.7306 (tp30) REVERT: O 99 THR cc_start: 0.7292 (p) cc_final: 0.6844 (p) REVERT: O 108 LYS cc_start: 0.8379 (ptmt) cc_final: 0.8015 (mptt) REVERT: P 122 TRP cc_start: 0.8742 (m100) cc_final: 0.8350 (m100) REVERT: Q 2 ILE cc_start: 0.8788 (mm) cc_final: 0.8524 (mm) REVERT: Q 78 ASN cc_start: 0.8709 (t0) cc_final: 0.7867 (t0) REVERT: R 1 GLN cc_start: 0.8141 (pm20) cc_final: 0.7589 (pm20) REVERT: R 122 TRP cc_start: 0.8692 (m100) cc_final: 0.8265 (m100) REVERT: S 38 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7966 (tm-30) REVERT: S 78 ASN cc_start: 0.8438 (t0) cc_final: 0.7241 (t0) REVERT: S 80 GLN cc_start: 0.8070 (mm110) cc_final: 0.7638 (mm-40) REVERT: T 111 LEU cc_start: 0.9362 (mm) cc_final: 0.8851 (mt) REVERT: U 38 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7957 (tm-30) REVERT: U 66 SER cc_start: 0.8651 (t) cc_final: 0.8263 (m) REVERT: U 78 ASN cc_start: 0.8494 (t0) cc_final: 0.7192 (t0) outliers start: 4 outliers final: 1 residues processed: 524 average time/residue: 0.1692 time to fit residues: 144.3369 Evaluate side-chains 408 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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: 3.9990 chunk 147 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 286 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 99 ASN ** 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** J 56 ASN K 7 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN M 33 ASN M 55 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN O 7 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095527 restraints weight = 51323.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098869 restraints weight = 34007.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099636 restraints weight = 24350.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099855 restraints weight = 19822.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100298 restraints weight = 18740.912| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26962 Z= 0.231 Angle : 0.910 13.228 36888 Z= 0.444 Chirality : 0.052 0.365 4503 Planarity : 0.006 0.106 4458 Dihedral : 6.492 41.876 3432 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.62 % Favored : 87.97 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.54 % 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 are not related in a simple way. whole: -3.18 (0.13), residues: 3183 helix: -0.16 (0.26), residues: 369 sheet: -1.08 (0.16), residues: 1008 loop : -3.32 (0.12), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 273 TYR 0.030 0.002 TYR F 484 PHE 0.039 0.003 PHE F 382 TRP 0.032 0.002 TRP R 122 HIS 0.011 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (26790) covalent geometry : angle 0.85559 / 0.43 (36429) SS BOND : bond 0.00635 / 0.43 ( 45) SS BOND : angle 1.83477 / 1.26 ( 90) hydrogen bonds : bond 0.04127 / 2.71 ( 779) hydrogen bonds : angle 5.96838 / 4.18 ( 2226) Misc. bond : bond 0.00034 / 0.02 ( 4) link_ALPHA1-2 : bond 0.00293 / 0.17 ( 9) link_ALPHA1-2 : angle 1.74776 / 1.29 ( 27) link_ALPHA1-3 : bond 0.00577 / 0.37 ( 12) link_ALPHA1-3 : angle 1.76095 / 1.17 ( 36) link_ALPHA1-6 : bond 0.00303 / 0.21 ( 9) link_ALPHA1-6 : angle 1.76782 / 1.29 ( 27) link_BETA1-4 : bond 0.00882 / 0.48 ( 39) link_BETA1-4 : angle 2.09492 / 1.45 ( 117) link_NAG-ASN : bond 0.00733 / 0.49 ( 54) link_NAG-ASN : angle 4.13891 / 3.06 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.88 seconds wall clock time: 79 minutes 44.18 seconds (4784.18 seconds total)