Starting phenix.real_space_refine on Fri Mar 6 19:36:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mw2_24060/03_2026/7mw2_24060.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw2_24060/03_2026/7mw2_24060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mw2_24060/03_2026/7mw2_24060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw2_24060/03_2026/7mw2_24060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mw2_24060/03_2026/7mw2_24060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw2_24060/03_2026/7mw2_24060.map" } resolution = 2.97 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 147 5.16 5 C 21459 2.51 5 N 5529 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33807 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "G" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 11.90, per 1000 atoms: 0.35 Number of scatterers: 33807 At special positions: 0 Unit cell: (138.84, 140.976, 222.144, 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 147 16.00 O 6672 8.00 N 5529 7.00 C 21459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.04 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 738 " - pdb=" SG CYS A 760 " 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=2.03 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 220 " distance=2.04 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=2.04 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 738 " - pdb=" SG CYS C 760 " 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 L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 220 " 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=2.04 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 738 " - pdb=" SG CYS B 760 " 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 158 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 164 " - pdb=" SG CYS F 220 " 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 BETA1-4 " 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-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 125 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 125 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C1074 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 234 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B 709 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 343 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 2.3 seconds 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8028 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 79 sheets defined 20.6% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.061A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.597A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.692A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.217A 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 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.566A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.713A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.601A 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.890A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.742A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.072A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.625A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.789A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.240A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 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 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.709A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.558A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.251A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.586A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.818A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.793A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'L' and resid 207 through 211 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 211 through 214 removed outlier: 4.295A pdb=" N GLY H 214 " --> pdb=" O SER H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.026A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.751A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.754A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.720A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.106A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.647A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.744A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.207A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.601A 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 984 removed outlier: 3.509A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.884A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.849A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 211 through 214 removed outlier: 4.188A pdb=" N GLY F 214 " --> pdb=" O SER F 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.700A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.220A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.188A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.965A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 319 removed outlier: 5.767A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.733A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.878A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.532A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.164A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'E' and resid 24 through 27 Processing sheet with id=AC2, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.386A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.386A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 121 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 138 through 142 removed outlier: 6.080A pdb=" N TYR E 197 " --> pdb=" O ASN E 162 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER E 198 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AC6, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.003A pdb=" N ALA D 125 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY D 119 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TRP D 127 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG D 117 " --> pdb=" O TRP D 127 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN D 129 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 115 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.030A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.030A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.254A pdb=" N TYR D 218 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.822A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.036A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.363A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.993A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 312 through 319 removed outlier: 6.030A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.239A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.751A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.561A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.152A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.286A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.286A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AF4, first strand: chain 'L' and resid 138 through 142 removed outlier: 5.948A pdb=" N TYR L 197 " --> pdb=" O ASN L 162 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER L 198 " --> pdb=" O THR L 188 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 177 through 178 Processing sheet with id=AF6, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AF7, first strand: chain 'H' and resid 29 through 31 removed outlier: 4.995A pdb=" N ALA H 125 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY H 119 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TRP H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG H 117 " --> pdb=" O TRP H 127 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN H 129 " --> pdb=" O CYS H 115 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS H 115 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.066A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.066A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 175 through 178 removed outlier: 4.172A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.781A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AG4, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.053A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.356A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.849A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 312 through 319 removed outlier: 5.925A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.693A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AG9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AH2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.377A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.249A 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: 6.904A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.377A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.186A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AH7, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH8, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.263A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.263A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 138 through 142 removed outlier: 6.070A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 198 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 168 through 174 Processing sheet with id=AI3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AI4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.993A pdb=" N ALA F 125 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY F 119 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TRP F 127 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG F 117 " --> pdb=" O TRP F 127 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN F 129 " --> pdb=" O CYS F 115 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS F 115 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR F 69 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.126A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.126A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 175 through 178 removed outlier: 4.218A pdb=" N TYR F 218 " --> pdb=" O VAL F 235 " (cutoff:3.500A) 1495 hydrogen bonds defined for protein. 4056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.73 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9292 1.33 - 1.46: 7322 1.46 - 1.58: 17766 1.58 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 34569 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 34564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 46132 2.12 - 4.24: 897 4.24 - 6.36: 78 6.36 - 8.48: 10 8.48 - 10.60: 4 Bond angle restraints: 47121 Sorted by residual: angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 111.77 103.74 8.03 1.04e+00 9.25e-01 5.96e+01 angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.77 104.57 7.20 1.04e+00 9.25e-01 4.79e+01 angle pdb=" N GLY C 502 " pdb=" CA GLY C 502 " pdb=" C GLY C 502 " ideal model delta sigma weight residual 111.93 106.87 5.06 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N GLY A 502 " pdb=" CA GLY A 502 " pdb=" C GLY A 502 " ideal model delta sigma weight residual 111.93 107.12 4.81 1.15e+00 7.56e-01 1.75e+01 angle pdb=" C GLN A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.85 115.66 4.19 1.01e+00 9.80e-01 1.72e+01 ... (remaining 47116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 20399 25.94 - 51.89: 818 51.89 - 77.83: 152 77.83 - 103.78: 64 103.78 - 129.72: 41 Dihedral angle restraints: 21474 sinusoidal: 8985 harmonic: 12489 Sorted by residual: dihedral pdb=" CA SER L 27 " pdb=" C SER L 27 " pdb=" N PRO L 28 " pdb=" CA PRO L 28 " ideal model delta harmonic sigma weight residual -180.00 -108.14 -71.86 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CA SER G 27 " pdb=" C SER G 27 " pdb=" N PRO G 28 " pdb=" CA PRO G 28 " ideal model delta harmonic sigma weight residual -180.00 -108.16 -71.84 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" CA SER E 27 " pdb=" C SER E 27 " pdb=" N PRO E 28 " pdb=" CA PRO E 28 " ideal model delta harmonic sigma weight residual -180.00 -108.38 -71.62 0 5.00e+00 4.00e-02 2.05e+02 ... (remaining 21471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.530: 5586 0.530 - 1.060: 3 1.060 - 1.590: 0 1.590 - 2.120: 2 2.120 - 2.650: 1 Chirality restraints: 5592 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 0.25 -2.65 2.00e-01 2.50e+01 1.76e+02 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.61 -1.79 2.00e-01 2.50e+01 7.99e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.66 -1.74 2.00e-01 2.50e+01 7.54e+01 ... (remaining 5589 not shown) Planarity restraints: 6051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " 0.249 2.00e-02 2.50e+03 2.12e-01 5.61e+02 pdb=" C7 NAG A1309 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " -0.363 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.245 2.00e-02 2.50e+03 2.08e-01 5.40e+02 pdb=" C7 NAG B1309 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.217 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG C1310 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.291 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " -0.022 2.00e-02 2.50e+03 ... (remaining 6048 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 4 2.23 - 2.89: 13237 2.89 - 3.56: 45476 3.56 - 4.23: 81907 4.23 - 4.90: 138772 Nonbonded interactions: 279396 Sorted by model distance: nonbonded pdb=" ND2 ASN B1074 " pdb=" C1 NAG B1310 " model vdw 1.558 3.550 nonbonded pdb=" ND2 ASN A1074 " pdb=" C1 NAG A1310 " model vdw 1.558 3.550 nonbonded pdb=" ND2 ASN C1074 " pdb=" C1 NAG C1310 " model vdw 1.570 3.550 nonbonded pdb=" OG SER C 591 " pdb=" OE2 GLU C 619 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.295 3.040 ... (remaining 279391 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1310)) selection = (chain 'B' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1310)) selection = (chain 'C' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1310)) } 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' } 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.650 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.170 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.004 0.116 34689 Z= 0.224 Angle : 0.820 35.787 47430 Z= 0.400 Chirality : 0.073 2.650 5592 Planarity : 0.007 0.212 6003 Dihedral : 16.064 129.723 13293 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.05 % 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: -0.24 (0.12), residues: 4233 helix: 0.52 (0.19), residues: 729 sheet: 0.56 (0.14), residues: 1323 loop : -0.83 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 44 TYR 0.019 0.001 TYR E 73 PHE 0.024 0.002 PHE A 906 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00429 (34569) covalent geometry : angle 0.68439 (47121) SS BOND : bond 0.00247 ( 51) SS BOND : angle 1.34197 ( 102) hydrogen bonds : bond 0.16399 ( 1400) hydrogen bonds : angle 7.71953 ( 4056) link_BETA1-4 : bond 0.00672 ( 21) link_BETA1-4 : angle 3.71584 ( 63) link_NAG-ASN : bond 0.03030 ( 48) link_NAG-ASN : angle 7.78555 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 MET cc_start: 0.7623 (tpt) cc_final: 0.7351 (tpp) REVERT: H 146 PHE cc_start: 0.6965 (m-10) cc_final: 0.6685 (m-10) REVERT: B 697 MET cc_start: 0.8578 (ptm) cc_final: 0.8226 (ptm) outliers start: 3 outliers final: 4 residues processed: 307 average time/residue: 0.6648 time to fit residues: 246.0690 Evaluate side-chains 231 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS C 901 GLN C1010 GLN A ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 901 GLN ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** 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 = 0.3554 r_free = 0.3554 target = 0.095303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065114 restraints weight = 119308.790| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.96 r_work: 0.2799 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34689 Z= 0.211 Angle : 0.772 18.475 47430 Z= 0.359 Chirality : 0.054 0.853 5592 Planarity : 0.005 0.066 6003 Dihedral : 13.249 103.839 6101 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.56 % Rotamer: Outliers : 1.70 % Allowed : 4.87 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.05 % 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: -0.14 (0.13), residues: 4233 helix: 1.34 (0.20), residues: 705 sheet: 0.49 (0.14), residues: 1344 loop : -0.96 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 44 TYR 0.027 0.002 TYR B1067 PHE 0.040 0.002 PHE C 906 TRP 0.019 0.002 TRP C 886 HIS 0.008 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00499 (34569) covalent geometry : angle 0.70075 (47121) SS BOND : bond 0.00279 ( 51) SS BOND : angle 1.55087 ( 102) hydrogen bonds : bond 0.04940 ( 1400) hydrogen bonds : angle 6.10100 ( 4056) link_BETA1-4 : bond 0.00298 ( 21) link_BETA1-4 : angle 2.31791 ( 63) link_NAG-ASN : bond 0.00939 ( 48) link_NAG-ASN : angle 5.61063 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6687 (tp30) cc_final: 0.6427 (tp30) REVERT: D 101 GLN cc_start: 0.7635 (tp-100) cc_final: 0.6976 (tp40) REVERT: D 224 HIS cc_start: 0.4842 (t-170) cc_final: 0.4618 (t70) REVERT: C 904 TYR cc_start: 0.8349 (m-10) cc_final: 0.8024 (m-10) REVERT: L 219 GLU cc_start: 0.6458 (tp30) cc_final: 0.6241 (tp30) REVERT: H 146 PHE cc_start: 0.7416 (m-10) cc_final: 0.7118 (m-10) REVERT: B 314 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: G 219 GLU cc_start: 0.6518 (tp30) cc_final: 0.6317 (tp30) REVERT: F 101 GLN cc_start: 0.8117 (tt0) cc_final: 0.7701 (tt0) REVERT: F 225 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7392 (tppp) outliers start: 58 outliers final: 27 residues processed: 279 average time/residue: 0.6757 time to fit residues: 225.4238 Evaluate side-chains 261 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 336 optimal weight: 2.9990 chunk 225 optimal weight: 0.2980 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 327 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 957 GLN A1010 GLN A ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065821 restraints weight = 136142.803| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.51 r_work: 0.2811 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34689 Z= 0.138 Angle : 0.717 17.717 47430 Z= 0.329 Chirality : 0.051 0.776 5592 Planarity : 0.005 0.062 6003 Dihedral : 11.794 98.114 6093 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 1.61 % Allowed : 6.48 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4233 helix: 1.71 (0.20), residues: 705 sheet: 0.46 (0.14), residues: 1344 loop : -0.96 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 44 TYR 0.022 0.001 TYR B 160 PHE 0.028 0.002 PHE C 133 TRP 0.014 0.001 TRP H 178 HIS 0.004 0.001 HIS H 188 Details of bonding type rmsd covalent geometry : bond 0.00315 (34569) covalent geometry : angle 0.64387 (47121) SS BOND : bond 0.00375 ( 51) SS BOND : angle 1.66409 ( 102) hydrogen bonds : bond 0.04233 ( 1400) hydrogen bonds : angle 5.76070 ( 4056) link_BETA1-4 : bond 0.00266 ( 21) link_BETA1-4 : angle 2.27745 ( 63) link_NAG-ASN : bond 0.00927 ( 48) link_NAG-ASN : angle 5.44291 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6784 (tp30) cc_final: 0.6520 (tp30) REVERT: D 172 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 224 HIS cc_start: 0.4959 (t-170) cc_final: 0.4621 (t70) REVERT: L 219 GLU cc_start: 0.6500 (tp30) cc_final: 0.6185 (tp30) REVERT: H 146 PHE cc_start: 0.7386 (m-10) cc_final: 0.7117 (m-10) REVERT: G 219 GLU cc_start: 0.6669 (tp30) cc_final: 0.6380 (tp30) REVERT: F 101 GLN cc_start: 0.8067 (tt0) cc_final: 0.7604 (tt0) REVERT: F 146 PHE cc_start: 0.7393 (m-10) cc_final: 0.7135 (m-10) REVERT: F 225 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7294 (tppp) outliers start: 55 outliers final: 22 residues processed: 273 average time/residue: 0.6562 time to fit residues: 215.6895 Evaluate side-chains 246 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 326 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 355 optimal weight: 0.0020 chunk 96 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 305 optimal weight: 0.1980 chunk 197 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065199 restraints weight = 138259.285| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.10 r_work: 0.2803 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 34689 Z= 0.155 Angle : 0.723 17.139 47430 Z= 0.333 Chirality : 0.051 0.759 5592 Planarity : 0.004 0.062 6003 Dihedral : 11.021 96.138 6093 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.08 % Favored : 96.71 % Rotamer: Outliers : 1.58 % Allowed : 7.67 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.02 % 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: -0.03 (0.13), residues: 4233 helix: 1.82 (0.20), residues: 705 sheet: 0.45 (0.14), residues: 1344 loop : -0.96 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 765 TYR 0.021 0.001 TYR B 160 PHE 0.030 0.002 PHE B 133 TRP 0.025 0.001 TRP H 178 HIS 0.003 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00363 (34569) covalent geometry : angle 0.65644 (47121) SS BOND : bond 0.00252 ( 51) SS BOND : angle 1.94180 ( 102) hydrogen bonds : bond 0.04169 ( 1400) hydrogen bonds : angle 5.64728 ( 4056) link_BETA1-4 : bond 0.00232 ( 21) link_BETA1-4 : angle 2.20890 ( 63) link_NAG-ASN : bond 0.00879 ( 48) link_NAG-ASN : angle 5.13507 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: E 219 GLU cc_start: 0.6859 (tp30) cc_final: 0.6520 (tp30) REVERT: D 101 GLN cc_start: 0.7490 (tp-100) cc_final: 0.6886 (tp40) REVERT: D 172 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8306 (mm-30) REVERT: D 224 HIS cc_start: 0.5177 (t-170) cc_final: 0.4960 (t70) REVERT: C 603 ASN cc_start: 0.7036 (m110) cc_final: 0.6354 (p0) REVERT: C 619 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6973 (pt0) REVERT: L 44 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7948 (mtp85) REVERT: L 142 PHE cc_start: 0.3510 (m-80) cc_final: 0.2875 (m-10) REVERT: L 219 GLU cc_start: 0.6646 (tp30) cc_final: 0.6282 (tp30) REVERT: H 146 PHE cc_start: 0.7379 (m-80) cc_final: 0.7017 (m-10) REVERT: B 314 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: G 142 PHE cc_start: 0.3748 (m-80) cc_final: 0.2913 (m-10) REVERT: G 219 GLU cc_start: 0.6920 (tp30) cc_final: 0.6545 (tp30) REVERT: F 101 GLN cc_start: 0.8072 (tt0) cc_final: 0.7647 (tt0) REVERT: F 146 PHE cc_start: 0.7421 (m-10) cc_final: 0.7159 (m-10) REVERT: F 225 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7253 (tppp) outliers start: 54 outliers final: 25 residues processed: 261 average time/residue: 0.6588 time to fit residues: 207.0112 Evaluate side-chains 249 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 294 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 HIS H 221 ASN B 81 ASN B 703 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063204 restraints weight = 163598.285| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.33 r_work: 0.2740 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34689 Z= 0.250 Angle : 0.768 16.864 47430 Z= 0.359 Chirality : 0.053 0.781 5592 Planarity : 0.005 0.065 6003 Dihedral : 10.528 94.669 6093 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.41 % Favored : 96.38 % Rotamer: Outliers : 1.78 % Allowed : 8.53 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.02 % 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: -0.17 (0.13), residues: 4233 helix: 1.64 (0.20), residues: 708 sheet: 0.34 (0.14), residues: 1347 loop : -1.00 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 44 TYR 0.020 0.002 TYR B1067 PHE 0.037 0.002 PHE B 133 TRP 0.026 0.002 TRP C 886 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00597 (34569) covalent geometry : angle 0.70582 (47121) SS BOND : bond 0.00411 ( 51) SS BOND : angle 1.73259 ( 102) hydrogen bonds : bond 0.04717 ( 1400) hydrogen bonds : angle 5.79723 ( 4056) link_BETA1-4 : bond 0.00221 ( 21) link_BETA1-4 : angle 2.22877 ( 63) link_NAG-ASN : bond 0.00778 ( 48) link_NAG-ASN : angle 5.19172 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1145 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7134 (tt) REVERT: E 219 GLU cc_start: 0.6847 (tp30) cc_final: 0.6163 (tp30) REVERT: D 101 GLN cc_start: 0.7396 (tp-100) cc_final: 0.6830 (tp40) REVERT: C 619 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: L 44 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8005 (mtp85) REVERT: L 219 GLU cc_start: 0.6776 (tp30) cc_final: 0.6337 (tp30) REVERT: H 146 PHE cc_start: 0.7409 (m-80) cc_final: 0.6982 (m-10) REVERT: B 314 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8533 (tm-30) REVERT: G 219 GLU cc_start: 0.6917 (tp30) cc_final: 0.6483 (tp30) REVERT: F 59 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7234 (mtp180) REVERT: F 101 GLN cc_start: 0.8158 (tt0) cc_final: 0.7766 (tt0) REVERT: F 225 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7201 (tppp) outliers start: 61 outliers final: 30 residues processed: 268 average time/residue: 0.6503 time to fit residues: 209.5074 Evaluate side-chains 261 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 94 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 408 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.065252 restraints weight = 145977.001| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.18 r_work: 0.2796 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34689 Z= 0.134 Angle : 0.714 16.425 47430 Z= 0.325 Chirality : 0.050 0.713 5592 Planarity : 0.004 0.061 6003 Dihedral : 9.633 92.221 6093 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.39 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 9.26 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.02 % 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: -0.07 (0.13), residues: 4233 helix: 1.88 (0.20), residues: 708 sheet: 0.35 (0.14), residues: 1353 loop : -0.97 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 44 TYR 0.025 0.001 TYR B 160 PHE 0.026 0.001 PHE F 146 TRP 0.024 0.001 TRP F 178 HIS 0.003 0.001 HIS F 188 Details of bonding type rmsd covalent geometry : bond 0.00306 (34569) covalent geometry : angle 0.64272 (47121) SS BOND : bond 0.00314 ( 51) SS BOND : angle 1.27753 ( 102) hydrogen bonds : bond 0.03934 ( 1400) hydrogen bonds : angle 5.54343 ( 4056) link_BETA1-4 : bond 0.00283 ( 21) link_BETA1-4 : angle 2.23029 ( 63) link_NAG-ASN : bond 0.00782 ( 48) link_NAG-ASN : angle 5.43485 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7428 (tp40) cc_final: 0.7177 (mm-40) REVERT: E 219 GLU cc_start: 0.6799 (tp30) cc_final: 0.6082 (tp30) REVERT: D 101 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6632 (tp40) REVERT: D 223 ASN cc_start: 0.6978 (t0) cc_final: 0.6731 (t0) REVERT: C 134 GLN cc_start: 0.7795 (tp40) cc_final: 0.7489 (mm110) REVERT: L 142 PHE cc_start: 0.3269 (m-10) cc_final: 0.2923 (m-10) REVERT: L 219 GLU cc_start: 0.6626 (tp30) cc_final: 0.6086 (tp30) REVERT: H 146 PHE cc_start: 0.7424 (m-80) cc_final: 0.6995 (m-10) REVERT: G 142 PHE cc_start: 0.3867 (m-10) cc_final: 0.3281 (m-10) REVERT: G 219 GLU cc_start: 0.6733 (tp30) cc_final: 0.6196 (tp30) REVERT: F 59 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7274 (mtp180) REVERT: F 101 GLN cc_start: 0.8095 (tt0) cc_final: 0.7656 (tt0) REVERT: F 146 PHE cc_start: 0.7100 (m-10) cc_final: 0.6839 (m-10) REVERT: F 221 ASN cc_start: 0.5938 (m110) cc_final: 0.5672 (m110) REVERT: F 225 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7130 (tppp) outliers start: 48 outliers final: 28 residues processed: 264 average time/residue: 0.6389 time to fit residues: 203.2560 Evaluate side-chains 256 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 347 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 302 optimal weight: 4.9990 chunk 384 optimal weight: 0.0050 chunk 424 optimal weight: 0.0970 chunk 423 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 221 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.064386 restraints weight = 133082.527| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.09 r_work: 0.2784 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34689 Z= 0.170 Angle : 0.717 15.762 47430 Z= 0.330 Chirality : 0.050 0.710 5592 Planarity : 0.005 0.062 6003 Dihedral : 9.265 91.778 6093 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 1.53 % Allowed : 9.84 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4233 helix: 1.87 (0.20), residues: 708 sheet: 0.32 (0.14), residues: 1323 loop : -0.97 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 44 TYR 0.020 0.001 TYR E 73 PHE 0.019 0.002 PHE F 146 TRP 0.027 0.002 TRP F 178 HIS 0.004 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00401 (34569) covalent geometry : angle 0.65074 (47121) SS BOND : bond 0.00285 ( 51) SS BOND : angle 1.26425 ( 102) hydrogen bonds : bond 0.04177 ( 1400) hydrogen bonds : angle 5.55769 ( 4056) link_BETA1-4 : bond 0.00232 ( 21) link_BETA1-4 : angle 2.22069 ( 63) link_NAG-ASN : bond 0.00825 ( 48) link_NAG-ASN : angle 5.21890 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7492 (tp40) cc_final: 0.7244 (mm-40) REVERT: A 218 GLN cc_start: 0.8467 (tt0) cc_final: 0.8241 (tm-30) REVERT: E 219 GLU cc_start: 0.6800 (tp30) cc_final: 0.6072 (tp30) REVERT: E 221 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7020 (p) REVERT: D 101 GLN cc_start: 0.7355 (tp-100) cc_final: 0.6801 (tp40) REVERT: C 134 GLN cc_start: 0.7907 (tp40) cc_final: 0.7602 (mm110) REVERT: C 1129 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8880 (m) REVERT: L 142 PHE cc_start: 0.3370 (m-10) cc_final: 0.2940 (m-10) REVERT: L 219 GLU cc_start: 0.6572 (tp30) cc_final: 0.6105 (tp30) REVERT: H 146 PHE cc_start: 0.7407 (m-80) cc_final: 0.6933 (m-10) REVERT: B 314 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: G 142 PHE cc_start: 0.3939 (m-10) cc_final: 0.3208 (m-10) REVERT: G 219 GLU cc_start: 0.6869 (tp30) cc_final: 0.6341 (tp30) REVERT: F 59 ARG cc_start: 0.7550 (mtp85) cc_final: 0.7276 (mtp180) REVERT: F 101 GLN cc_start: 0.8158 (tt0) cc_final: 0.7736 (tt0) REVERT: F 146 PHE cc_start: 0.7029 (m-10) cc_final: 0.6703 (m-10) REVERT: F 225 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7138 (tppp) outliers start: 52 outliers final: 35 residues processed: 267 average time/residue: 0.6621 time to fit residues: 212.1632 Evaluate side-chains 266 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 83 optimal weight: 1.9990 chunk 326 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 231 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 221 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.064891 restraints weight = 159862.966| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.39 r_work: 0.2789 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34689 Z= 0.122 Angle : 0.688 15.336 47430 Z= 0.316 Chirality : 0.048 0.674 5592 Planarity : 0.004 0.081 6003 Dihedral : 8.886 90.707 6093 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.28 % Rotamer: Outliers : 1.25 % Allowed : 10.43 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.13), residues: 4233 helix: 2.00 (0.20), residues: 705 sheet: 0.41 (0.14), residues: 1311 loop : -0.93 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG L 44 TYR 0.023 0.001 TYR E 73 PHE 0.021 0.001 PHE C 133 TRP 0.032 0.001 TRP F 178 HIS 0.003 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00275 (34569) covalent geometry : angle 0.62347 (47121) SS BOND : bond 0.00236 ( 51) SS BOND : angle 1.20376 ( 102) hydrogen bonds : bond 0.03824 ( 1400) hydrogen bonds : angle 5.43555 ( 4056) link_BETA1-4 : bond 0.00337 ( 21) link_BETA1-4 : angle 2.25008 ( 63) link_NAG-ASN : bond 0.00767 ( 48) link_NAG-ASN : angle 5.03675 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6866 (tp30) cc_final: 0.6121 (tp30) REVERT: E 221 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7073 (p) REVERT: D 101 GLN cc_start: 0.7212 (tp-100) cc_final: 0.6516 (tp-100) REVERT: C 134 GLN cc_start: 0.7777 (tp40) cc_final: 0.7480 (mm110) REVERT: L 142 PHE cc_start: 0.3348 (m-10) cc_final: 0.2992 (m-10) REVERT: L 219 GLU cc_start: 0.6638 (tp30) cc_final: 0.6139 (tp30) REVERT: H 146 PHE cc_start: 0.7405 (m-80) cc_final: 0.6907 (m-10) REVERT: B 808 ASP cc_start: 0.7255 (t0) cc_final: 0.7003 (t0) REVERT: G 142 PHE cc_start: 0.3868 (m-10) cc_final: 0.3304 (m-10) REVERT: G 219 GLU cc_start: 0.6916 (tp30) cc_final: 0.6391 (tp30) REVERT: F 59 ARG cc_start: 0.7474 (mtp85) cc_final: 0.7233 (mtp180) REVERT: F 101 GLN cc_start: 0.8073 (tt0) cc_final: 0.7619 (tt0) REVERT: F 146 PHE cc_start: 0.7064 (m-10) cc_final: 0.6727 (m-10) REVERT: F 225 LYS cc_start: 0.7256 (tppp) cc_final: 0.6964 (mppt) outliers start: 42 outliers final: 29 residues processed: 260 average time/residue: 0.6350 time to fit residues: 199.6854 Evaluate side-chains 255 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 223 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 345 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 398 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 199 optimal weight: 0.4980 chunk 327 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 221 ASN B 580 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** 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 = 0.3525 r_free = 0.3525 target = 0.092894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.063378 restraints weight = 135963.840| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.10 r_work: 0.2755 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 34689 Z= 0.238 Angle : 0.754 14.952 47430 Z= 0.354 Chirality : 0.051 0.704 5592 Planarity : 0.005 0.063 6003 Dihedral : 8.961 92.149 6093 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.91 % Favored : 95.88 % Rotamer: Outliers : 1.42 % Allowed : 10.45 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4233 helix: 1.71 (0.20), residues: 708 sheet: 0.26 (0.14), residues: 1320 loop : -0.99 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 44 TYR 0.025 0.002 TYR E 73 PHE 0.024 0.002 PHE C 906 TRP 0.035 0.002 TRP F 178 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00566 (34569) covalent geometry : angle 0.69433 (47121) SS BOND : bond 0.00315 ( 51) SS BOND : angle 1.34480 ( 102) hydrogen bonds : bond 0.04615 ( 1400) hydrogen bonds : angle 5.67909 ( 4056) link_BETA1-4 : bond 0.00255 ( 21) link_BETA1-4 : angle 2.27371 ( 63) link_NAG-ASN : bond 0.00739 ( 48) link_NAG-ASN : angle 5.08496 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6983 (tp30) cc_final: 0.6212 (tp30) REVERT: E 221 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7097 (p) REVERT: D 101 GLN cc_start: 0.7211 (tp-100) cc_final: 0.6724 (tp40) REVERT: D 223 ASN cc_start: 0.6995 (t0) cc_final: 0.6758 (t0) REVERT: C 134 GLN cc_start: 0.7786 (tp40) cc_final: 0.7436 (mm110) REVERT: C 1129 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8874 (m) REVERT: L 44 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7971 (ttm110) REVERT: L 142 PHE cc_start: 0.3488 (m-10) cc_final: 0.2908 (m-10) REVERT: L 219 GLU cc_start: 0.6664 (tp30) cc_final: 0.6144 (tp30) REVERT: H 146 PHE cc_start: 0.7412 (m-80) cc_final: 0.6910 (m-10) REVERT: B 314 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: B 1129 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8882 (t) REVERT: G 142 PHE cc_start: 0.3999 (m-10) cc_final: 0.3279 (m-10) REVERT: G 219 GLU cc_start: 0.6843 (tp30) cc_final: 0.6319 (tp30) REVERT: F 59 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7200 (mtp180) REVERT: F 101 GLN cc_start: 0.8142 (tt0) cc_final: 0.7788 (tt0) REVERT: F 146 PHE cc_start: 0.7111 (m-10) cc_final: 0.6725 (m-10) REVERT: F 225 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7143 (tppp) outliers start: 48 outliers final: 34 residues processed: 263 average time/residue: 0.6390 time to fit residues: 202.3578 Evaluate side-chains 264 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 367 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 281 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 403 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 209 optimal weight: 0.0980 chunk 399 optimal weight: 0.3980 chunk 96 optimal weight: 0.0010 chunk 402 optimal weight: 7.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.065176 restraints weight = 141300.885| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.21 r_work: 0.2806 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 34689 Z= 0.119 Angle : 0.700 17.023 47430 Z= 0.323 Chirality : 0.051 1.278 5592 Planarity : 0.004 0.061 6003 Dihedral : 8.684 93.438 6093 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.41 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 10.87 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4233 helix: 1.97 (0.20), residues: 705 sheet: 0.35 (0.14), residues: 1314 loop : -0.96 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 44 TYR 0.026 0.001 TYR E 73 PHE 0.021 0.001 PHE C 133 TRP 0.044 0.002 TRP F 178 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00262 (34569) covalent geometry : angle 0.63551 (47121) SS BOND : bond 0.00221 ( 51) SS BOND : angle 1.04182 ( 102) hydrogen bonds : bond 0.03798 ( 1400) hydrogen bonds : angle 5.45540 ( 4056) link_BETA1-4 : bond 0.00346 ( 21) link_BETA1-4 : angle 2.32356 ( 63) link_NAG-ASN : bond 0.00776 ( 48) link_NAG-ASN : angle 5.10145 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9154 (mtp) cc_final: 0.8906 (mtp) REVERT: E 219 GLU cc_start: 0.6929 (tp30) cc_final: 0.6188 (tp30) REVERT: E 221 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7085 (p) REVERT: D 101 GLN cc_start: 0.7146 (tp-100) cc_final: 0.6566 (tp40) REVERT: D 223 ASN cc_start: 0.7191 (t0) cc_final: 0.6891 (t0) REVERT: C 134 GLN cc_start: 0.7758 (tp40) cc_final: 0.7469 (mm110) REVERT: L 44 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7967 (ttm110) REVERT: L 142 PHE cc_start: 0.3320 (m-10) cc_final: 0.2978 (m-10) REVERT: L 219 GLU cc_start: 0.6665 (tp30) cc_final: 0.6146 (tp30) REVERT: H 146 PHE cc_start: 0.7437 (m-80) cc_final: 0.6935 (m-10) REVERT: G 142 PHE cc_start: 0.3949 (m-10) cc_final: 0.3346 (m-10) REVERT: G 219 GLU cc_start: 0.6865 (tp30) cc_final: 0.6354 (tp30) REVERT: F 59 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7237 (mtp180) REVERT: F 101 GLN cc_start: 0.8057 (tt0) cc_final: 0.7614 (tt0) REVERT: F 146 PHE cc_start: 0.7114 (m-10) cc_final: 0.6730 (m-10) REVERT: F 225 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6968 (mppt) outliers start: 37 outliers final: 26 residues processed: 251 average time/residue: 0.6592 time to fit residues: 199.2711 Evaluate side-chains 250 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 345 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 GLN H 22 GLN H 188 HIS B 134 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064622 restraints weight = 118570.901| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.91 r_work: 0.2790 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34689 Z= 0.180 Angle : 0.710 14.459 47430 Z= 0.331 Chirality : 0.050 0.668 5592 Planarity : 0.005 0.061 6003 Dihedral : 8.525 90.825 6093 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.67 % Favored : 96.11 % Rotamer: Outliers : 1.14 % Allowed : 10.98 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4233 helix: 1.87 (0.20), residues: 708 sheet: 0.30 (0.14), residues: 1314 loop : -0.97 (0.12), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 44 TYR 0.029 0.001 TYR E 73 PHE 0.019 0.002 PHE D 146 TRP 0.040 0.002 TRP F 178 HIS 0.003 0.001 HIS F 224 Details of bonding type rmsd covalent geometry : bond 0.00425 (34569) covalent geometry : angle 0.65199 (47121) SS BOND : bond 0.00266 ( 51) SS BOND : angle 1.15241 ( 102) hydrogen bonds : bond 0.04191 ( 1400) hydrogen bonds : angle 5.51182 ( 4056) link_BETA1-4 : bond 0.00274 ( 21) link_BETA1-4 : angle 2.28850 ( 63) link_NAG-ASN : bond 0.00681 ( 48) link_NAG-ASN : angle 4.86781 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11054.25 seconds wall clock time: 188 minutes 52.64 seconds (11332.64 seconds total)