Starting phenix.real_space_refine on Mon Jul 6 11:47:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.map" model { file = "/net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mw6_24064/07_2026/7mw6_24064.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 22362 2.51 5 N 5778 2.21 5 O 6954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35247 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 8166 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8157 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8157 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8338 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8153 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8153 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8334 Chain: "B" Number of atoms: 8170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8161 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8161 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8342 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 Time building chain proxies: 12.54, per 1000 atoms: 0.36 Number of scatterers: 35247 At special positions: 0 Unit cell: (168.744, 156.996, 247.776, 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 153 16.00 O 6954 8.00 N 5778 7.00 C 22362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.04 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 190 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 245 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG j 1 " - " NAG j 2 " " NAG p 1 " - " NAG p 2 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 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 o 1 " - " NAG o 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A1074 " " NAG A1307 " - " ASN A 234 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C1074 " " NAG C1307 " - " ASN C 234 " " NAG I 1 " - " ASN A 61 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 122 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 709 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN C 61 " " NAG V 1 " - " ASN C 282 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 709 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 17 " " NAG f 1 " - " ASN B 61 " " NAG g 1 " - " ASN B 282 " " NAG h 1 " - " ASN B 122 " " NAG i 1 " - " ASN B 331 " " NAG j 1 " - " ASN B1134 " " NAG k 1 " - " ASN B1098 " " NAG l 1 " - " ASN B 801 " " NAG m 1 " - " ASN B 717 " " NAG n 1 " - " ASN B 709 " " NAG o 1 " - " ASN B 343 " " NAG p 1 " - " ASN B 17 " Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 2.3 seconds 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8298 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 80 sheets defined 19.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.503A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.622A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.375A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.654A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.599A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.502A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 removed outlier: 3.670A pdb=" N GLN A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 941 removed outlier: 5.883A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.528A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.565A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.526A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.411A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 236 through 240 removed outlier: 4.240A pdb=" N GLY D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 236 through 240' Processing helix chain 'L' and resid 172 through 179 removed outlier: 3.669A pdb=" N GLY L 179 " --> pdb=" O GLN L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'H' and resid 236 through 242 removed outlier: 4.031A pdb=" N GLY H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.329A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.751A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.017A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.631A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.852A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.618A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.577A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 916 through 920 removed outlier: 3.572A pdb=" N GLN C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 6.340A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.758A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.107A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.559A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.513A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.543A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.847A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.611A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.726A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 removed outlier: 3.585A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 920 removed outlier: 3.506A pdb=" N GLN B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 941 removed outlier: 5.910A pdb=" N PHE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.571A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.555A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.741A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.458A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'F' and resid 236 through 242 removed outlier: 4.106A pdb=" N GLY F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.972A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.789A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.383A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.311A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 328 removed outlier: 4.823A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.654A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 728 removed outlier: 7.126A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.880A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1080 through 1082 Processing sheet with id=AB9, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'E' and resid 30 through 33 Processing sheet with id=AC3, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'E' and resid 165 through 169 removed outlier: 3.819A pdb=" N SER E 165 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 226 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN E 189 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E 224 " --> pdb=" O ASN E 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 195 through 201 Processing sheet with id=AC6, first strand: chain 'D' and resid 24 through 26 removed outlier: 4.006A pdb=" N SER D 40 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.617A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET D 53 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.085A pdb=" N TYR D 226 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.085A pdb=" N TYR D 226 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 201 through 204 removed outlier: 4.727A pdb=" N TYR D 244 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 25 through 27 Processing sheet with id=AD3, first strand: chain 'L' and resid 30 through 33 removed outlier: 3.667A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR L 110 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN L 61 " --> pdb=" O LYS L 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AD5, first strand: chain 'L' and resid 165 through 169 removed outlier: 3.988A pdb=" N SER L 165 " --> pdb=" O ASN L 188 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER L 182 " --> pdb=" O LEU L 232 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU L 232 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL L 184 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU L 230 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 186 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER L 228 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN L 188 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU L 226 " --> pdb=" O ASN L 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 195 through 201 Processing sheet with id=AD7, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.883A pdb=" N SER H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.891A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET H 53 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.991A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.991A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 201 through 204 removed outlier: 4.603A pdb=" N TYR H 244 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.024A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.045A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.914A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.862A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.042A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.004A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.212A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.091A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.819A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.960A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AG2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.873A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.773A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AG7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.454A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.766A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.335A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.575A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.042A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.338A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AH7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AH8, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH9, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.873A pdb=" N GLN G 58 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AI2, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.201A pdb=" N SER G 182 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU G 232 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL G 184 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU G 230 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU G 186 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER G 228 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASN G 188 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU G 226 " --> pdb=" O ASN G 188 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 195 through 201 Processing sheet with id=AI4, first strand: chain 'F' and resid 24 through 26 removed outlier: 4.090A pdb=" N SER F 40 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.727A pdb=" N TRP F 66 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.134A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.134A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 201 through 204 removed outlier: 4.556A pdb=" N TYR F 244 " --> pdb=" O VAL F 261 " (cutoff:3.500A) 1342 hydrogen bonds defined for protein. 3612 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: 10.20 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5970 1.32 - 1.45: 9923 1.45 - 1.57: 19944 1.57 - 1.70: 1 1.70 - 1.82: 198 Bond restraints: 36036 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 36031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.67: 49069 8.67 - 17.35: 5 17.35 - 26.02: 2 26.02 - 34.70: 0 34.70 - 43.37: 1 Bond angle restraints: 49077 Sorted by residual: angle pdb=" C LEU B 24 " pdb=" N PRO B 25 " pdb=" CD PRO B 25 " ideal model delta sigma weight residual 125.00 81.63 43.37 4.10e+00 5.95e-02 1.12e+02 angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 111.33 121.92 -10.59 1.43e+00 4.89e-01 5.49e+01 angle pdb=" C GLY C 252 " pdb=" N ASP C 253 " pdb=" CA ASP C 253 " ideal model delta sigma weight residual 121.54 134.78 -13.24 1.91e+00 2.74e-01 4.81e+01 angle pdb=" N GLU B1072 " pdb=" CA GLU B1072 " pdb=" C GLU B1072 " ideal model delta sigma weight residual 110.80 125.51 -14.71 2.13e+00 2.20e-01 4.77e+01 angle pdb=" C SER H 118 " pdb=" CA SER H 118 " pdb=" CB SER H 118 " ideal model delta sigma weight residual 116.54 109.49 7.05 1.15e+00 7.56e-01 3.76e+01 ... (remaining 49072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19113 17.98 - 35.95: 1357 35.95 - 53.93: 223 53.93 - 71.91: 61 71.91 - 89.89: 15 Dihedral angle restraints: 20769 sinusoidal: 7860 harmonic: 12909 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.60 -88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA LYS C 811 " pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta harmonic sigma weight residual 180.00 135.55 44.45 0 5.00e+00 4.00e-02 7.90e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 20766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.527: 5832 0.527 - 1.055: 6 1.055 - 1.582: 2 1.582 - 2.110: 0 2.110 - 2.637: 4 Chirality restraints: 5844 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 0.24 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 0.12 -2.52 2.00e-01 2.50e+01 1.59e+02 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 0.09 -2.49 2.00e-01 2.50e+01 1.56e+02 ... (remaining 5841 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.301 2.00e-02 2.50e+03 2.58e-01 8.33e+02 pdb=" C7 NAG B1305 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.261 2.00e-02 2.50e+03 2.18e-01 5.91e+02 pdb=" C7 NAG B1302 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.363 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.256 2.00e-02 2.50e+03 2.13e-01 5.67e+02 pdb=" C7 NAG C1302 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.008 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 12 2.22 - 2.89: 14085 2.89 - 3.56: 48445 3.56 - 4.23: 84213 4.23 - 4.90: 140536 Nonbonded interactions: 287291 Sorted by model distance: nonbonded pdb=" ND2 ASN B1074 " pdb=" C1 NAG B1305 " model vdw 1.556 3.550 nonbonded pdb=" ND2 ASN A1074 " pdb=" C1 NAG A1306 " model vdw 1.561 3.550 nonbonded pdb=" ND2 ASN C1074 " pdb=" C1 NAG C1306 " model vdw 1.562 3.550 nonbonded pdb=" O GLY F 27 " pdb=" OG1 THR F 127 " model vdw 2.093 3.040 nonbonded pdb=" OD1 ASN C 125 " pdb=" O3 NAG W 1 " model vdw 2.104 3.040 ... (remaining 287286 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' and (resid 15 through 181 or (resid 182 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 416 or (resid 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 100 \ 9 or resid 1011 through 1307)) selection = (chain 'B' and (resid 15 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 416 \ or (resid 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 through 1009 or resid 1011 through 1307)) selection = (chain 'C' and (resid 15 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 1009 or resid 1011 through 1307 \ )) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 42.990 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.005 0.119 36171 Z= 0.246 Angle : 0.967 43.373 49431 Z= 0.476 Chirality : 0.092 2.637 5844 Planarity : 0.010 0.258 6213 Dihedral : 12.896 89.886 12318 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.08 % Favored : 94.23 % Rotamer: Outliers : 0.13 % Allowed : 0.35 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4395 helix: -0.07 (0.19), residues: 725 sheet: -0.07 (0.14), residues: 1321 loop : -1.41 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 117 TYR 0.023 0.002 TYR L 73 PHE 0.039 0.002 PHE B 135 TRP 0.037 0.002 TRP A 152 HIS 0.011 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (36036) covalent geometry : angle 0.83744 / 0.45 (49077) SS BOND : bond 0.00298 / 0.20 ( 51) SS BOND : angle 1.14722 / 0.81 ( 102) hydrogen bonds : bond 0.15577 / 10.08 ( 1291) hydrogen bonds : angle 7.69251 / 5.28 ( 3612) link_BETA1-3 : bond 0.01732 / 0.85 ( 2) link_BETA1-3 : angle 2.31527 / 1.01 ( 6) link_BETA1-4 : bond 0.00648 / 0.44 ( 31) link_BETA1-4 : angle 2.43507 / 1.59 ( 93) link_NAG-ASN : bond 0.03151 / 1.98 ( 51) link_NAG-ASN : angle 8.49841 / 5.24 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8302 (mp) cc_final: 0.7753 (mp) REVERT: E 22 ILE cc_start: 0.6684 (mp) cc_final: 0.6401 (mp) REVERT: D 125 GLN cc_start: 0.6810 (pm20) cc_final: 0.6603 (pm20) REVERT: L 59 TRP cc_start: 0.6417 (m-10) cc_final: 0.5848 (m-10) REVERT: C 105 ILE cc_start: 0.8255 (mm) cc_final: 0.8043 (mm) REVERT: B 490 PHE cc_start: 0.7173 (t80) cc_final: 0.6938 (t80) REVERT: F 250 HIS cc_start: -0.0180 (t-170) cc_final: -0.0855 (t-90) outliers start: 2 outliers final: 1 residues processed: 421 average time/residue: 0.2054 time to fit residues: 145.2899 Evaluate side-chains 331 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0570 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN C 66 HIS C 394 ASN C 965 GLN B 394 ASN B 901 GLN G 175 GLN ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.112534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086621 restraints weight = 152534.771| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 4.47 r_work: 0.2733 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 36171 Z= 0.179 Angle : 0.805 25.458 49431 Z= 0.384 Chirality : 0.056 0.645 5844 Planarity : 0.007 0.181 6213 Dihedral : 5.878 54.314 4739 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.70 % Favored : 93.64 % Rotamer: Outliers : 0.61 % Allowed : 6.51 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 4395 helix: 0.82 (0.20), residues: 704 sheet: -0.15 (0.14), residues: 1350 loop : -1.31 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 117 TYR 0.032 0.002 TYR E 73 PHE 0.032 0.002 PHE C 133 TRP 0.040 0.002 TRP A 258 HIS 0.012 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (36036) covalent geometry : angle 0.74264 / 0.37 (49077) SS BOND : bond 0.00349 / 0.21 ( 51) SS BOND : angle 1.03801 / 0.69 ( 102) hydrogen bonds : bond 0.04610 / 3.09 ( 1291) hydrogen bonds : angle 6.20415 / 4.29 ( 3612) link_BETA1-3 : bond 0.01276 / 0.62 ( 2) link_BETA1-3 : angle 2.22809 / 0.95 ( 6) link_BETA1-4 : bond 0.00577 / 0.39 ( 31) link_BETA1-4 : angle 1.81712 / 1.23 ( 93) link_NAG-ASN : bond 0.01091 / 0.77 ( 51) link_NAG-ASN : angle 5.42343 / 3.40 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 366 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 TYR cc_start: 0.7808 (m-80) cc_final: 0.7486 (m-80) REVERT: D 55 TRP cc_start: 0.7990 (m100) cc_final: 0.7524 (m100) REVERT: D 100 MET cc_start: 0.8666 (tmm) cc_final: 0.7819 (tmm) REVERT: L 60 TYR cc_start: 0.8188 (m-80) cc_final: 0.7752 (m-10) REVERT: L 94 ASP cc_start: 0.7742 (m-30) cc_final: 0.7452 (m-30) REVERT: H 24 GLN cc_start: 0.6816 (mp10) cc_final: 0.6613 (mp10) REVERT: H 99 TYR cc_start: 0.7268 (m-10) cc_final: 0.6957 (m-10) REVERT: H 100 MET cc_start: 0.7743 (tmm) cc_final: 0.7519 (tmm) REVERT: H 216 PHE cc_start: 0.6058 (m-80) cc_final: 0.5650 (m-80) REVERT: C 400 PHE cc_start: 0.9030 (p90) cc_final: 0.8790 (p90) REVERT: C 486 PHE cc_start: 0.8600 (m-10) cc_final: 0.8307 (m-10) REVERT: B 63 THR cc_start: 0.9046 (m) cc_final: 0.8745 (p) REVERT: G 224 TYR cc_start: 0.7202 (m-80) cc_final: 0.6933 (m-80) REVERT: F 117 ARG cc_start: 0.7793 (tmm-80) cc_final: 0.7181 (ttm-80) REVERT: F 250 HIS cc_start: 0.1069 (t-170) cc_final: -0.0447 (t-90) outliers start: 20 outliers final: 13 residues processed: 374 average time/residue: 0.1991 time to fit residues: 125.6659 Evaluate side-chains 338 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 325 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 125 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 422 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 347 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN H 71 ASN H 125 GLN C 66 HIS C 125 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.111019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084842 restraints weight = 140375.110| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.35 r_work: 0.2745 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 36171 Z= 0.169 Angle : 0.762 19.859 49431 Z= 0.367 Chirality : 0.055 0.629 5844 Planarity : 0.006 0.155 6213 Dihedral : 5.730 42.798 4737 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.24 % Favored : 94.09 % Rotamer: Outliers : 0.75 % Allowed : 8.33 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4395 helix: 1.06 (0.20), residues: 704 sheet: -0.13 (0.14), residues: 1357 loop : -1.25 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 117 TYR 0.023 0.002 TYR E 73 PHE 0.027 0.002 PHE D 48 TRP 0.032 0.002 TRP A 258 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (36036) covalent geometry : angle 0.70606 / 0.35 (49077) SS BOND : bond 0.00276 / 0.17 ( 51) SS BOND : angle 1.12043 / 0.71 ( 102) hydrogen bonds : bond 0.04269 / 2.86 ( 1291) hydrogen bonds : angle 5.95727 / 4.12 ( 3612) link_BETA1-3 : bond 0.01132 / 0.56 ( 2) link_BETA1-3 : angle 1.95592 / 0.84 ( 6) link_BETA1-4 : bond 0.00546 / 0.37 ( 31) link_BETA1-4 : angle 1.75423 / 1.20 ( 93) link_NAG-ASN : bond 0.01001 / 0.69 ( 51) link_NAG-ASN : angle 4.96264 / 3.09 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 364 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 TRP cc_start: 0.7759 (m100) cc_final: 0.7326 (m100) REVERT: D 56 MET cc_start: 0.7739 (mmt) cc_final: 0.7467 (mmm) REVERT: D 79 ASP cc_start: 0.7666 (t0) cc_final: 0.7405 (t0) REVERT: D 117 ARG cc_start: 0.7168 (ttt90) cc_final: 0.6206 (ttt90) REVERT: D 196 PHE cc_start: 0.6476 (t80) cc_final: 0.6242 (t80) REVERT: L 60 TYR cc_start: 0.8149 (m-80) cc_final: 0.7847 (m-10) REVERT: H 24 GLN cc_start: 0.6947 (mp10) cc_final: 0.6743 (mp10) REVERT: H 56 MET cc_start: 0.8155 (mmm) cc_final: 0.7751 (mmm) REVERT: H 100 MET cc_start: 0.7802 (tmm) cc_final: 0.7549 (tmm) REVERT: H 216 PHE cc_start: 0.5853 (m-80) cc_final: 0.5391 (m-80) REVERT: C 396 TYR cc_start: 0.8406 (m-80) cc_final: 0.8078 (m-80) REVERT: C 486 PHE cc_start: 0.8534 (m-10) cc_final: 0.8266 (m-80) REVERT: B 102 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8176 (mtt-85) REVERT: G 41 ILE cc_start: 0.8517 (mt) cc_final: 0.8309 (mm) REVERT: G 224 TYR cc_start: 0.7021 (m-80) cc_final: 0.6815 (m-80) REVERT: F 92 ASP cc_start: 0.8003 (m-30) cc_final: 0.7681 (m-30) REVERT: F 121 ASP cc_start: 0.8441 (p0) cc_final: 0.8201 (p0) outliers start: 25 outliers final: 14 residues processed: 380 average time/residue: 0.1933 time to fit residues: 123.0646 Evaluate side-chains 355 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 340 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 101 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 260 optimal weight: 0.1980 chunk 343 optimal weight: 5.9990 chunk 341 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 245 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 362 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN B B 388 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.111328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085730 restraints weight = 146457.830| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.27 r_work: 0.2731 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 36171 Z= 0.156 Angle : 0.741 19.718 49431 Z= 0.356 Chirality : 0.054 0.584 5844 Planarity : 0.006 0.147 6213 Dihedral : 5.627 41.807 4737 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.45 % Favored : 93.91 % Rotamer: Outliers : 0.99 % Allowed : 9.95 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 4395 helix: 1.10 (0.20), residues: 716 sheet: -0.09 (0.14), residues: 1342 loop : -1.25 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 44 TYR 0.025 0.001 TYR E 73 PHE 0.027 0.002 PHE D 83 TRP 0.027 0.002 TRP A 258 HIS 0.007 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (36036) covalent geometry : angle 0.68956 / 0.35 (49077) SS BOND : bond 0.00244 / 0.16 ( 51) SS BOND : angle 0.92280 / 0.60 ( 102) hydrogen bonds : bond 0.04014 / 2.69 ( 1291) hydrogen bonds : angle 5.79768 / 4.00 ( 3612) link_BETA1-3 : bond 0.01148 / 0.56 ( 2) link_BETA1-3 : angle 1.78350 / 0.78 ( 6) link_BETA1-4 : bond 0.00560 / 0.37 ( 31) link_BETA1-4 : angle 1.71099 / 1.17 ( 93) link_NAG-ASN : bond 0.00961 / 0.67 ( 51) link_NAG-ASN : angle 4.71244 / 2.93 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 366 time to evaluate : 1.390 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: D 53 MET cc_start: 0.8903 (tpt) cc_final: 0.8626 (tpp) REVERT: D 56 MET cc_start: 0.7798 (mmt) cc_final: 0.7488 (mmm) REVERT: D 117 ARG cc_start: 0.7209 (ttt90) cc_final: 0.6664 (ttt90) REVERT: D 196 PHE cc_start: 0.6533 (t80) cc_final: 0.6307 (t80) REVERT: L 72 ILE cc_start: 0.9172 (mm) cc_final: 0.8470 (tp) REVERT: L 116 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: H 24 GLN cc_start: 0.6976 (mp10) cc_final: 0.6697 (mp10) REVERT: H 56 MET cc_start: 0.8170 (mmm) cc_final: 0.7665 (mmm) REVERT: H 100 MET cc_start: 0.8048 (tmm) cc_final: 0.7742 (tmm) REVERT: H 125 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: H 216 PHE cc_start: 0.5876 (m-80) cc_final: 0.5382 (m-80) REVERT: C 396 TYR cc_start: 0.8484 (m-80) cc_final: 0.8043 (m-80) REVERT: B 102 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (mtt-85) REVERT: F 92 ASP cc_start: 0.8020 (m-30) cc_final: 0.7548 (m-30) REVERT: F 121 ASP cc_start: 0.8374 (p0) cc_final: 0.8095 (p0) outliers start: 34 outliers final: 21 residues processed: 385 average time/residue: 0.1974 time to fit residues: 127.9634 Evaluate side-chains 369 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 346 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 101 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 2.9990 chunk 225 optimal weight: 0.0970 chunk 255 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 410 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN L 217 GLN C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS B 394 ASN B1010 GLN B ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.110188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.082057 restraints weight = 132845.340| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.29 r_work: 0.2695 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 36171 Z= 0.246 Angle : 0.804 25.238 49431 Z= 0.388 Chirality : 0.056 0.564 5844 Planarity : 0.006 0.182 6213 Dihedral : 5.840 43.737 4737 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.06 % Favored : 93.37 % Rotamer: Outliers : 1.55 % Allowed : 10.57 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.83 (0.12), residues: 4395 helix: 0.85 (0.20), residues: 721 sheet: -0.13 (0.14), residues: 1367 loop : -1.28 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1039 TYR 0.024 0.002 TYR C1067 PHE 0.028 0.002 PHE C 906 TRP 0.035 0.002 TRP A 258 HIS 0.010 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (36036) covalent geometry : angle 0.75386 / 0.38 (49077) SS BOND : bond 0.00349 / 0.23 ( 51) SS BOND : angle 0.95755 / 0.65 ( 102) hydrogen bonds : bond 0.04555 / 3.05 ( 1291) hydrogen bonds : angle 5.84898 / 4.04 ( 3612) link_BETA1-3 : bond 0.01028 / 0.52 ( 2) link_BETA1-3 : angle 1.86018 / 0.88 ( 6) link_BETA1-4 : bond 0.00504 / 0.33 ( 31) link_BETA1-4 : angle 1.86584 / 1.26 ( 93) link_NAG-ASN : bond 0.00993 / 0.66 ( 51) link_NAG-ASN : angle 4.86596 / 3.03 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 367 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 MET cc_start: 0.8878 (tpt) cc_final: 0.8644 (tpp) REVERT: D 100 MET cc_start: 0.8619 (tmm) cc_final: 0.7761 (tmm) REVERT: D 117 ARG cc_start: 0.7240 (ttt90) cc_final: 0.6821 (ttt180) REVERT: L 217 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7076 (tp40) REVERT: L 224 TYR cc_start: 0.7170 (m-10) cc_final: 0.6735 (m-10) REVERT: H 24 GLN cc_start: 0.7095 (mp10) cc_final: 0.6887 (mp10) REVERT: H 100 MET cc_start: 0.8056 (tmm) cc_final: 0.7656 (tmm) REVERT: H 125 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: H 216 PHE cc_start: 0.6038 (m-80) cc_final: 0.5516 (m-80) REVERT: C 455 LEU cc_start: 0.9010 (mp) cc_final: 0.8682 (mp) REVERT: B 102 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8296 (mtt-85) REVERT: B 505 TYR cc_start: 0.8598 (t80) cc_final: 0.8192 (t80) REVERT: F 46 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.4469 (t80) outliers start: 55 outliers final: 29 residues processed: 400 average time/residue: 0.2028 time to fit residues: 136.7188 Evaluate side-chains 369 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 336 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 217 GLN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 125 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 101 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 108 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 291 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 286 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 GLN H 125 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.110611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087576 restraints weight = 172813.406| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 5.02 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 36171 Z= 0.171 Angle : 0.759 19.625 49431 Z= 0.363 Chirality : 0.054 0.559 5844 Planarity : 0.006 0.160 6213 Dihedral : 5.719 42.236 4737 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.75 % Favored : 93.68 % Rotamer: Outliers : 1.28 % Allowed : 11.56 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 4395 helix: 1.20 (0.20), residues: 692 sheet: -0.12 (0.14), residues: 1373 loop : -1.22 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 44 TYR 0.021 0.002 TYR F 122 PHE 0.031 0.002 PHE F 48 TRP 0.045 0.002 TRP B 258 HIS 0.019 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (36036) covalent geometry : angle 0.71069 / 0.35 (49077) SS BOND : bond 0.00255 / 0.17 ( 51) SS BOND : angle 0.89710 / 0.61 ( 102) hydrogen bonds : bond 0.04073 / 2.73 ( 1291) hydrogen bonds : angle 5.71551 / 3.95 ( 3612) link_BETA1-3 : bond 0.01064 / 0.53 ( 2) link_BETA1-3 : angle 1.61373 / 0.74 ( 6) link_BETA1-4 : bond 0.00522 / 0.33 ( 31) link_BETA1-4 : angle 1.73085 / 1.17 ( 93) link_NAG-ASN : bond 0.00979 / 0.65 ( 51) link_NAG-ASN : angle 4.64232 / 2.88 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 346 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ASP cc_start: 0.6550 (m-30) cc_final: 0.6339 (m-30) outliers start: 45 outliers final: 31 residues processed: 374 average time/residue: 0.2022 time to fit residues: 127.5854 Evaluate side-chains 357 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 122 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 209 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 393 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 415 optimal weight: 20.0000 chunk 367 optimal weight: 0.2980 chunk 172 optimal weight: 0.1980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 GLN F 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.108856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084961 restraints weight = 157523.611| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.57 r_work: 0.2628 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 36171 Z= 0.340 Angle : 0.885 19.692 49431 Z= 0.430 Chirality : 0.060 0.518 5844 Planarity : 0.007 0.151 6213 Dihedral : 6.094 45.808 4737 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.89 % Favored : 92.52 % Rotamer: Outliers : 1.49 % Allowed : 12.01 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4395 helix: 0.70 (0.19), residues: 699 sheet: -0.26 (0.13), residues: 1406 loop : -1.27 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 102 TYR 0.042 0.002 TYR E 191 PHE 0.034 0.003 PHE A 133 TRP 0.029 0.003 TRP A 258 HIS 0.012 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.34 (36036) covalent geometry : angle 0.83539 / 0.42 (49077) SS BOND : bond 0.00415 / 0.27 ( 51) SS BOND : angle 1.03567 / 0.70 ( 102) hydrogen bonds : bond 0.04980 / 3.34 ( 1291) hydrogen bonds : angle 5.97753 / 4.13 ( 3612) link_BETA1-3 : bond 0.00831 / 0.42 ( 2) link_BETA1-3 : angle 1.99581 / 0.99 ( 6) link_BETA1-4 : bond 0.00511 / 0.34 ( 31) link_BETA1-4 : angle 2.09400 / 1.39 ( 93) link_NAG-ASN : bond 0.01011 / 0.66 ( 51) link_NAG-ASN : angle 5.08261 / 3.17 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7601 (pm20) REVERT: D 29 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7817 (mm-30) REVERT: D 100 MET cc_start: 0.8633 (tmm) cc_final: 0.7806 (tmm) REVERT: D 196 PHE cc_start: 0.7014 (t80) cc_final: 0.6665 (t80) REVERT: L 106 ASP cc_start: 0.7117 (m-30) cc_final: 0.6875 (m-30) REVERT: H 125 GLN cc_start: 0.7813 (pm20) cc_final: 0.7480 (pm20) REVERT: H 216 PHE cc_start: 0.6066 (m-10) cc_final: 0.5856 (m-80) REVERT: C 133 PHE cc_start: 0.8553 (m-80) cc_final: 0.7998 (m-80) REVERT: C 387 LEU cc_start: 0.8563 (mt) cc_final: 0.8204 (mt) REVERT: C 455 LEU cc_start: 0.8949 (mp) cc_final: 0.8383 (mt) REVERT: C 493 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8112 (pp30) REVERT: B 164 ASN cc_start: 0.8043 (p0) cc_final: 0.7666 (p0) REVERT: B 178 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (p0) REVERT: B 409 GLN cc_start: 0.8615 (tt0) cc_final: 0.8379 (tt0) REVERT: G 190 PHE cc_start: 0.6589 (p90) cc_final: 0.5382 (p90) REVERT: F 25 GLN cc_start: 0.6988 (pt0) cc_final: 0.6616 (pt0) REVERT: F 46 TYR cc_start: 0.5639 (OUTLIER) cc_final: 0.4944 (t80) outliers start: 53 outliers final: 39 residues processed: 386 average time/residue: 0.1873 time to fit residues: 123.1103 Evaluate side-chains 376 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 422 optimal weight: 2.9990 chunk 369 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 342 optimal weight: 4.9990 chunk 426 optimal weight: 20.0000 chunk 131 optimal weight: 0.0670 chunk 102 optimal weight: 0.8980 chunk 371 optimal weight: 0.6980 chunk 372 optimal weight: 0.8980 chunk 358 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN F 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.110828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083883 restraints weight = 138647.582| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.39 r_work: 0.2735 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36171 Z= 0.137 Angle : 0.755 19.547 49431 Z= 0.360 Chirality : 0.052 0.499 5844 Planarity : 0.006 0.148 6213 Dihedral : 5.678 41.078 4737 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.31 % Favored : 94.12 % Rotamer: Outliers : 1.12 % Allowed : 12.54 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4395 helix: 1.29 (0.20), residues: 690 sheet: -0.18 (0.14), residues: 1376 loop : -1.21 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 102 TYR 0.027 0.001 TYR E 73 PHE 0.018 0.001 PHE A 79 TRP 0.028 0.002 TRP A 258 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (36036) covalent geometry : angle 0.71008 / 0.35 (49077) SS BOND : bond 0.00232 / 0.16 ( 51) SS BOND : angle 0.88247 / 0.60 ( 102) hydrogen bonds : bond 0.03836 / 2.57 ( 1291) hydrogen bonds : angle 5.67430 / 3.93 ( 3612) link_BETA1-3 : bond 0.01023 / 0.51 ( 2) link_BETA1-3 : angle 1.58229 / 0.71 ( 6) link_BETA1-4 : bond 0.00573 / 0.38 ( 31) link_BETA1-4 : angle 1.64772 / 1.14 ( 93) link_NAG-ASN : bond 0.00976 / 0.65 ( 51) link_NAG-ASN : angle 4.47196 / 2.77 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 345 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7722 (mmp) cc_final: 0.7293 (ptp) REVERT: D 56 MET cc_start: 0.7670 (mmt) cc_final: 0.7281 (mmm) REVERT: D 100 MET cc_start: 0.8610 (tmm) cc_final: 0.7900 (tmm) REVERT: D 196 PHE cc_start: 0.6906 (t80) cc_final: 0.6623 (t80) REVERT: L 73 TYR cc_start: 0.8089 (m-80) cc_final: 0.7865 (m-80) REVERT: L 106 ASP cc_start: 0.7100 (m-30) cc_final: 0.6868 (m-30) REVERT: H 216 PHE cc_start: 0.6024 (m-10) cc_final: 0.5720 (m-80) REVERT: C 338 PHE cc_start: 0.8757 (m-80) cc_final: 0.8416 (m-80) REVERT: C 387 LEU cc_start: 0.8477 (mt) cc_final: 0.8120 (mt) REVERT: B 178 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8472 (p0) REVERT: G 190 PHE cc_start: 0.6118 (p90) cc_final: 0.5018 (p90) REVERT: F 25 GLN cc_start: 0.6822 (pt0) cc_final: 0.6503 (pt0) REVERT: F 46 TYR cc_start: 0.5516 (OUTLIER) cc_final: 0.4990 (t80) REVERT: F 53 MET cc_start: 0.7956 (tpt) cc_final: 0.7740 (tpp) REVERT: F 92 ASP cc_start: 0.7906 (m-30) cc_final: 0.7221 (m-30) outliers start: 39 outliers final: 32 residues processed: 369 average time/residue: 0.2048 time to fit residues: 128.8641 Evaluate side-chains 371 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 115 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 297 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.110021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085685 restraints weight = 155993.605| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.43 r_work: 0.2685 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36171 Z= 0.210 Angle : 0.786 19.566 49431 Z= 0.379 Chirality : 0.054 0.479 5844 Planarity : 0.006 0.150 6213 Dihedral : 5.738 43.185 4737 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.02 % Favored : 93.39 % Rotamer: Outliers : 1.09 % Allowed : 12.62 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4395 helix: 1.17 (0.20), residues: 697 sheet: -0.19 (0.14), residues: 1382 loop : -1.21 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 102 TYR 0.023 0.002 TYR C1067 PHE 0.031 0.002 PHE A 133 TRP 0.024 0.002 TRP A 258 HIS 0.008 0.001 HIS F 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (36036) covalent geometry : angle 0.74046 / 0.37 (49077) SS BOND : bond 0.00272 / 0.18 ( 51) SS BOND : angle 0.89290 / 0.61 ( 102) hydrogen bonds : bond 0.04258 / 2.86 ( 1291) hydrogen bonds : angle 5.69537 / 3.93 ( 3612) link_BETA1-3 : bond 0.00934 / 0.47 ( 2) link_BETA1-3 : angle 1.57509 / 0.76 ( 6) link_BETA1-4 : bond 0.00469 / 0.32 ( 31) link_BETA1-4 : angle 1.78814 / 1.21 ( 93) link_NAG-ASN : bond 0.00914 / 0.60 ( 51) link_NAG-ASN : angle 4.57401 / 2.85 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7676 (mmp) cc_final: 0.7276 (ptp) REVERT: A 410 ILE cc_start: 0.9488 (mm) cc_final: 0.9218 (mt) REVERT: D 56 MET cc_start: 0.7702 (mmt) cc_final: 0.7392 (mmm) REVERT: D 79 ASP cc_start: 0.7884 (t70) cc_final: 0.7638 (t0) REVERT: D 196 PHE cc_start: 0.6870 (t80) cc_final: 0.6549 (t80) REVERT: L 73 TYR cc_start: 0.8102 (m-80) cc_final: 0.7864 (m-80) REVERT: L 106 ASP cc_start: 0.7142 (m-30) cc_final: 0.6881 (m-30) REVERT: H 100 MET cc_start: 0.7854 (tmm) cc_final: 0.7281 (tmm) REVERT: H 123 TRP cc_start: 0.8473 (m-10) cc_final: 0.8225 (m-10) REVERT: H 125 GLN cc_start: 0.7617 (pm20) cc_final: 0.7415 (pm20) REVERT: H 216 PHE cc_start: 0.6120 (m-10) cc_final: 0.5805 (m-80) REVERT: C 133 PHE cc_start: 0.8524 (m-80) cc_final: 0.8153 (m-80) REVERT: C 387 LEU cc_start: 0.8515 (mt) cc_final: 0.8146 (mt) REVERT: C 493 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8065 (pp30) REVERT: B 178 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8593 (p0) REVERT: B 380 TYR cc_start: 0.8778 (m-10) cc_final: 0.8461 (m-10) REVERT: G 190 PHE cc_start: 0.6285 (p90) cc_final: 0.5178 (p90) REVERT: F 25 GLN cc_start: 0.6918 (pt0) cc_final: 0.6632 (pt0) REVERT: F 46 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4828 (t80) REVERT: F 53 MET cc_start: 0.7960 (tpt) cc_final: 0.7725 (tpp) REVERT: F 71 ASN cc_start: 0.7724 (t0) cc_final: 0.7369 (t0) REVERT: F 204 TRP cc_start: 0.4695 (m100) cc_final: 0.4159 (m100) outliers start: 38 outliers final: 35 residues processed: 365 average time/residue: 0.1974 time to fit residues: 123.4556 Evaluate side-chains 370 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 333 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 115 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 375 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 422 optimal weight: 8.9990 chunk 327 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 355 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.111117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084135 restraints weight = 150051.120| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.58 r_work: 0.2717 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36171 Z= 0.138 Angle : 0.740 19.404 49431 Z= 0.354 Chirality : 0.051 0.455 5844 Planarity : 0.006 0.149 6213 Dihedral : 5.502 39.912 4737 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.38 % Favored : 94.03 % Rotamer: Outliers : 1.07 % Allowed : 12.81 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4395 helix: 1.43 (0.20), residues: 702 sheet: -0.10 (0.14), residues: 1358 loop : -1.23 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 102 TYR 0.027 0.001 TYR F 99 PHE 0.019 0.001 PHE H 196 TRP 0.026 0.002 TRP F 66 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (36036) covalent geometry : angle 0.69749 / 0.34 (49077) SS BOND : bond 0.00224 / 0.15 ( 51) SS BOND : angle 0.86128 / 0.58 ( 102) hydrogen bonds : bond 0.03696 / 2.48 ( 1291) hydrogen bonds : angle 5.54365 / 3.83 ( 3612) link_BETA1-3 : bond 0.01110 / 0.56 ( 2) link_BETA1-3 : angle 1.48034 / 0.68 ( 6) link_BETA1-4 : bond 0.00562 / 0.37 ( 31) link_BETA1-4 : angle 1.62849 / 1.12 ( 93) link_NAG-ASN : bond 0.00920 / 0.61 ( 51) link_NAG-ASN : angle 4.30890 / 2.67 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 348 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8570 (m-10) cc_final: 0.8334 (m-10) REVERT: A 153 MET cc_start: 0.7702 (mmp) cc_final: 0.7270 (ptp) REVERT: A 410 ILE cc_start: 0.9487 (mm) cc_final: 0.9204 (mt) REVERT: D 29 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7012 (mp0) REVERT: D 55 TRP cc_start: 0.7837 (m100) cc_final: 0.7093 (m100) REVERT: D 56 MET cc_start: 0.7604 (mmt) cc_final: 0.7318 (mmm) REVERT: D 79 ASP cc_start: 0.7887 (t70) cc_final: 0.7674 (t0) REVERT: D 196 PHE cc_start: 0.6919 (t80) cc_final: 0.6604 (t80) REVERT: L 73 TYR cc_start: 0.8033 (m-80) cc_final: 0.7765 (m-80) REVERT: L 106 ASP cc_start: 0.7130 (m-30) cc_final: 0.6878 (m-30) REVERT: H 100 MET cc_start: 0.7966 (tmm) cc_final: 0.7377 (tmm) REVERT: H 123 TRP cc_start: 0.8527 (m-10) cc_final: 0.8241 (m-10) REVERT: H 196 PHE cc_start: 0.7421 (t80) cc_final: 0.7213 (t80) REVERT: H 216 PHE cc_start: 0.6204 (m-10) cc_final: 0.5855 (m-80) REVERT: C 133 PHE cc_start: 0.8528 (m-80) cc_final: 0.8064 (m-80) REVERT: C 338 PHE cc_start: 0.8742 (m-80) cc_final: 0.8350 (m-80) REVERT: C 387 LEU cc_start: 0.8507 (mt) cc_final: 0.8128 (mt) REVERT: B 178 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8591 (p0) REVERT: B 380 TYR cc_start: 0.8842 (m-10) cc_final: 0.8617 (m-10) REVERT: G 190 PHE cc_start: 0.6417 (p90) cc_final: 0.5300 (p90) REVERT: F 25 GLN cc_start: 0.7004 (pt0) cc_final: 0.6729 (pt0) REVERT: F 46 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4701 (t80) REVERT: F 53 MET cc_start: 0.7859 (tpt) cc_final: 0.7653 (tpp) REVERT: F 58 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7917 (tp40) REVERT: F 71 ASN cc_start: 0.7557 (t0) cc_final: 0.7175 (t0) REVERT: F 204 TRP cc_start: 0.4651 (m100) cc_final: 0.4108 (m100) outliers start: 37 outliers final: 33 residues processed: 372 average time/residue: 0.2031 time to fit residues: 129.6173 Evaluate side-chains 375 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 115 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 268 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 405 optimal weight: 0.9980 chunk 402 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 762 GLN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.111097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086083 restraints weight = 157185.789| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.55 r_work: 0.2713 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36171 Z= 0.141 Angle : 0.731 19.317 49431 Z= 0.350 Chirality : 0.051 0.442 5844 Planarity : 0.006 0.149 6213 Dihedral : 5.393 40.053 4737 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.72 % Favored : 93.68 % Rotamer: Outliers : 0.99 % Allowed : 12.89 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4395 helix: 1.43 (0.20), residues: 708 sheet: -0.07 (0.14), residues: 1367 loop : -1.20 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 117 TYR 0.024 0.001 TYR E 73 PHE 0.022 0.001 PHE G 111 TRP 0.024 0.002 TRP A 258 HIS 0.006 0.001 HIS F 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (36036) covalent geometry : angle 0.68996 / 0.34 (49077) SS BOND : bond 0.00206 / 0.14 ( 51) SS BOND : angle 0.84895 / 0.57 ( 102) hydrogen bonds : bond 0.03678 / 2.48 ( 1291) hydrogen bonds : angle 5.47175 / 3.77 ( 3612) link_BETA1-3 : bond 0.00962 / 0.48 ( 2) link_BETA1-3 : angle 1.38126 / 0.64 ( 6) link_BETA1-4 : bond 0.00514 / 0.35 ( 31) link_BETA1-4 : angle 1.63809 / 1.12 ( 93) link_NAG-ASN : bond 0.00883 / 0.58 ( 51) link_NAG-ASN : angle 4.24058 / 2.63 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9925.39 seconds wall clock time: 170 minutes 41.36 seconds (10241.36 seconds total)