Starting phenix.real_space_refine on Fri Oct 30 04:30:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.map" model { file = "/net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw6_24064/10_2026/7mw6_24064.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 22362 2.51 5 N 5778 2.21 5 O 6954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35247 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 8166 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8157 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8157 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8338 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8153 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8153 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8334 Chain: "B" Number of atoms: 8170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8161 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 1058, 8161 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 8342 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 Time building chain proxies: 12.50, per 1000 atoms: 0.35 Number of scatterers: 35247 At special positions: 0 Unit cell: (168.744, 156.996, 247.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 6954 8.00 N 5778 7.00 C 22362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.04 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 190 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 245 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG j 1 " - " NAG j 2 " " NAG p 1 " - " NAG p 2 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 234 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 234 " " NAG I 1 " - " ASN A 61 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 122 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 709 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN C 61 " " NAG V 1 " - " ASN C 282 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 709 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 17 " " NAG f 1 " - " ASN B 61 " " NAG g 1 " - " ASN B 282 " " NAG h 1 " - " ASN B 122 " " NAG i 1 " - " ASN B 331 " " NAG j 1 " - " ASN B1134 " " NAG k 1 " - " ASN B1098 " " NAG l 1 " - " ASN B 801 " " NAG m 1 " - " ASN B 717 " " NAG n 1 " - " ASN B 709 " " NAG o 1 " - " ASN B 343 " " NAG p 1 " - " ASN B 17 " Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 2.5 seconds 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8298 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 80 sheets defined 19.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.503A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.622A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.375A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.654A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.599A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.502A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 removed outlier: 3.670A pdb=" N GLN A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 941 removed outlier: 5.883A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.528A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.565A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.526A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.411A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 236 through 240 removed outlier: 4.240A pdb=" N GLY D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 236 through 240' Processing helix chain 'L' and resid 172 through 179 removed outlier: 3.669A pdb=" N GLY L 179 " --> pdb=" O GLN L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'H' and resid 236 through 242 removed outlier: 4.031A pdb=" N GLY H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.329A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.751A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.017A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.631A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.852A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.618A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.577A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 916 through 920 removed outlier: 3.572A pdb=" N GLN C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 6.340A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.758A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.107A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.559A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.513A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.543A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.847A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.611A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.726A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 removed outlier: 3.585A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 920 removed outlier: 3.506A pdb=" N GLN B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 941 removed outlier: 5.910A pdb=" N PHE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.571A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.555A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.741A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.458A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'F' and resid 236 through 242 removed outlier: 4.106A pdb=" N GLY F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.972A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.789A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.383A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.311A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 328 removed outlier: 4.823A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.654A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 728 removed outlier: 7.126A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.880A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1080 through 1082 Processing sheet with id=AB9, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'E' and resid 30 through 33 Processing sheet with id=AC3, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'E' and resid 165 through 169 removed outlier: 3.819A pdb=" N SER E 165 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 226 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN E 189 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E 224 " --> pdb=" O ASN E 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 195 through 201 Processing sheet with id=AC6, first strand: chain 'D' and resid 24 through 26 removed outlier: 4.006A pdb=" N SER D 40 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.617A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET D 53 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.085A pdb=" N TYR D 226 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.085A pdb=" N TYR D 226 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 201 through 204 removed outlier: 4.727A pdb=" N TYR D 244 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 25 through 27 Processing sheet with id=AD3, first strand: chain 'L' and resid 30 through 33 removed outlier: 3.667A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR L 110 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN L 61 " --> pdb=" O LYS L 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AD5, first strand: chain 'L' and resid 165 through 169 removed outlier: 3.988A pdb=" N SER L 165 " --> pdb=" O ASN L 188 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER L 182 " --> pdb=" O LEU L 232 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU L 232 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL L 184 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU L 230 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 186 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER L 228 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN L 188 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU L 226 " --> pdb=" O ASN L 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 195 through 201 Processing sheet with id=AD7, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.883A pdb=" N SER H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.891A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET H 53 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.991A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.991A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 201 through 204 removed outlier: 4.603A pdb=" N TYR H 244 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.024A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.045A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.914A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.862A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.042A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.004A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.212A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.091A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.819A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.960A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AG2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.873A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.773A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AG7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.454A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.766A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.335A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.575A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 721 through 728 removed outlier: 7.042A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.338A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AH7, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AH8, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH9, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.873A pdb=" N GLN G 58 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AI2, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.201A pdb=" N SER G 182 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU G 232 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL G 184 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU G 230 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU G 186 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER G 228 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASN G 188 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU G 226 " --> pdb=" O ASN G 188 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 195 through 201 Processing sheet with id=AI4, first strand: chain 'F' and resid 24 through 26 removed outlier: 4.090A pdb=" N SER F 40 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.727A pdb=" N TRP F 66 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.134A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.134A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 201 through 204 removed outlier: 4.556A pdb=" N TYR F 244 " --> pdb=" O VAL F 261 " (cutoff:3.500A) 1342 hydrogen bonds defined for protein. 3612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.06 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5970 1.32 - 1.45: 9923 1.45 - 1.57: 19944 1.57 - 1.70: 1 1.70 - 1.82: 198 Bond restraints: 36036 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 36031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.67: 49069 8.67 - 17.35: 5 17.35 - 26.02: 2 26.02 - 34.70: 0 34.70 - 43.37: 1 Bond angle restraints: 49077 Sorted by residual: angle pdb=" C LEU B 24 " pdb=" N PRO B 25 " pdb=" CD PRO B 25 " ideal model delta sigma weight residual 125.00 81.63 43.37 4.10e+00 5.95e-02 1.12e+02 angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 111.33 121.92 -10.59 1.43e+00 4.89e-01 5.49e+01 angle pdb=" C GLY C 252 " pdb=" N ASP C 253 " pdb=" CA ASP C 253 " ideal model delta sigma weight residual 121.54 134.78 -13.24 1.91e+00 2.74e-01 4.81e+01 angle pdb=" N GLU B1072 " pdb=" CA GLU B1072 " pdb=" C GLU B1072 " ideal model delta sigma weight residual 110.80 125.51 -14.71 2.13e+00 2.20e-01 4.77e+01 angle pdb=" C SER H 118 " pdb=" CA SER H 118 " pdb=" CB SER H 118 " ideal model delta sigma weight residual 116.54 109.49 7.05 1.15e+00 7.56e-01 3.76e+01 ... (remaining 49072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19113 17.98 - 35.95: 1357 35.95 - 53.93: 223 53.93 - 71.91: 61 71.91 - 89.89: 15 Dihedral angle restraints: 20769 sinusoidal: 7860 harmonic: 12909 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 -178.60 -88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA LYS C 811 " pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta harmonic sigma weight residual 180.00 135.55 44.45 0 5.00e+00 4.00e-02 7.90e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 20766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.527: 5832 0.527 - 1.055: 8 1.055 - 1.582: 2 1.582 - 2.110: 0 2.110 - 2.637: 5 Chirality restraints: 5847 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 0.24 -2.64 2.00e-01 2.50e+01 1.74e+02 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 0.12 -2.52 2.00e-01 2.50e+01 1.59e+02 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 0.09 -2.49 2.00e-01 2.50e+01 1.56e+02 ... (remaining 5844 not shown) Planarity restraints: 6267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.301 2.00e-02 2.50e+03 2.58e-01 8.33e+02 pdb=" C7 NAG B1305 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.261 2.00e-02 2.50e+03 2.18e-01 5.91e+02 pdb=" C7 NAG B1302 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.363 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.256 2.00e-02 2.50e+03 2.13e-01 5.67e+02 pdb=" C7 NAG C1302 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " -0.008 2.00e-02 2.50e+03 ... (remaining 6264 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 492 2.65 - 3.22: 32900 3.22 - 3.78: 53920 3.78 - 4.34: 76670 4.34 - 4.90: 123294 Nonbonded interactions: 287276 Sorted by model distance: nonbonded pdb=" O GLY F 27 " pdb=" OG1 THR F 127 " model vdw 2.093 3.040 nonbonded pdb=" OD1 ASN C 125 " pdb=" O3 NAG W 1 " model vdw 2.104 3.040 nonbonded pdb=" O GLY D 27 " pdb=" OG1 THR D 127 " model vdw 2.159 3.040 nonbonded pdb=" O GLN C 913 " pdb=" N VAL C 915 " model vdw 2.165 3.120 nonbonded pdb=" O GLN B 913 " pdb=" N VAL B 915 " model vdw 2.166 3.120 ... (remaining 287271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 181 or (resid 182 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 416 or (resid 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 100 \ 9 or resid 1011 through 1307)) selection = (chain 'B' and (resid 15 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 416 \ or (resid 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 through 1009 or resid 1011 through 1307)) selection = (chain 'C' and (resid 15 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 1009 or resid 1011 through 1307 \ )) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 42.150 Find NCS groups from input model: 0.990 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 36174 Z= 0.252 Angle : 0.999 43.373 49440 Z= 0.484 Chirality : 0.097 2.637 5847 Planarity : 0.010 0.258 6213 Dihedral : 12.896 89.886 12318 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.08 % Favored : 94.23 % Rotamer: Outliers : 0.13 % Allowed : 0.35 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4395 helix: -0.07 (0.19), residues: 725 sheet: -0.07 (0.14), residues: 1321 loop : -1.41 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 117 TYR 0.023 0.002 TYR L 73 PHE 0.039 0.002 PHE B 135 TRP 0.037 0.002 TRP A 152 HIS 0.011 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (36036) covalent geometry : angle 0.83744 / 0.45 (49077) SS BOND : bond 0.00298 / 0.20 ( 51) SS BOND : angle 1.14722 / 0.81 ( 102) hydrogen bonds : bond 0.15577 / 10.08 ( 1291) hydrogen bonds : angle 7.69251 / 5.28 ( 3612) link_BETA1-3 : bond 0.01732 / 0.85 ( 2) link_BETA1-3 : angle 2.31527 / 1.01 ( 6) link_BETA1-4 : bond 0.00648 / 0.44 ( 31) link_BETA1-4 : angle 2.43507 / 1.59 ( 93) link_NAG-ASN : bond 0.04179 / 3.11 ( 54) link_NAG-ASN : angle 9.37526 / 5.89 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8302 (mp) cc_final: 0.7753 (mp) REVERT: E 22 ILE cc_start: 0.6684 (mp) cc_final: 0.6401 (mp) REVERT: D 125 GLN cc_start: 0.6810 (pm20) cc_final: 0.6603 (pm20) REVERT: L 59 TRP cc_start: 0.6417 (m-10) cc_final: 0.5848 (m-10) REVERT: C 105 ILE cc_start: 0.8255 (mm) cc_final: 0.8043 (mm) REVERT: B 490 PHE cc_start: 0.7173 (t80) cc_final: 0.6938 (t80) REVERT: F 250 HIS cc_start: -0.0180 (t-170) cc_final: -0.0855 (t-90) outliers start: 2 outliers final: 1 residues processed: 421 average time/residue: 0.2026 time to fit residues: 143.3079 Evaluate side-chains 331 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0570 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN C 66 HIS C 394 ASN C 965 GLN B 394 ASN B 901 GLN ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.111523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085568 restraints weight = 150851.881| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.42 r_work: 0.2745 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 36174 Z= 0.179 Angle : 0.813 25.349 49440 Z= 0.386 Chirality : 0.057 0.810 5847 Planarity : 0.007 0.181 6213 Dihedral : 5.857 44.882 4739 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.65 % Favored : 93.66 % Rotamer: Outliers : 0.64 % Allowed : 6.46 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 4395 helix: 0.82 (0.20), residues: 704 sheet: -0.15 (0.14), residues: 1350 loop : -1.32 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 117 TYR 0.033 0.002 TYR E 73 PHE 0.034 0.002 PHE A 906 TRP 0.040 0.002 TRP A 258 HIS 0.013 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (36036) covalent geometry : angle 0.75135 / 0.37 (49077) SS BOND : bond 0.00303 / 0.19 ( 51) SS BOND : angle 1.04497 / 0.69 ( 102) hydrogen bonds : bond 0.04541 / 3.04 ( 1291) hydrogen bonds : angle 6.18929 / 4.27 ( 3612) link_BETA1-3 : bond 0.01283 / 0.62 ( 2) link_BETA1-3 : angle 2.19196 / 0.94 ( 6) link_BETA1-4 : bond 0.00540 / 0.37 ( 31) link_BETA1-4 : angle 1.81030 / 1.23 ( 93) link_NAG-ASN : bond 0.01334 / 1.00 ( 54) link_NAG-ASN : angle 5.27635 / 3.34 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 369 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 TYR cc_start: 0.7747 (m-80) cc_final: 0.7471 (m-80) REVERT: D 55 TRP cc_start: 0.7958 (m100) cc_final: 0.7418 (m100) REVERT: D 100 MET cc_start: 0.8659 (tmm) cc_final: 0.7870 (tmm) REVERT: L 94 ASP cc_start: 0.7655 (m-30) cc_final: 0.7388 (m-30) REVERT: H 100 MET cc_start: 0.7570 (tmm) cc_final: 0.7353 (tmm) REVERT: H 216 PHE cc_start: 0.6021 (m-80) cc_final: 0.5630 (m-80) REVERT: C 378 LYS cc_start: 0.8466 (tptm) cc_final: 0.8224 (tptm) REVERT: C 400 PHE cc_start: 0.8977 (p90) cc_final: 0.8746 (p90) REVERT: C 486 PHE cc_start: 0.8482 (m-10) cc_final: 0.8220 (m-10) REVERT: B 63 THR cc_start: 0.9023 (m) cc_final: 0.8739 (p) REVERT: F 117 ARG cc_start: 0.7762 (tmm-80) cc_final: 0.7209 (ttm-80) REVERT: F 250 HIS cc_start: 0.0856 (t-170) cc_final: -0.0593 (t-90) outliers start: 21 outliers final: 15 residues processed: 378 average time/residue: 0.1887 time to fit residues: 120.8798 Evaluate side-chains 343 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 328 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 125 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [422, 34, 18, 347, 159, 308, 258, 133, 201, 237, 180] chunk 422 optimal weight: 10.0000 chunk 34 optimal weight: 0.0470 chunk 18 optimal weight: 10.0000 chunk 347 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 overall best weight: 2.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN L 250 GLN H 71 ASN H 125 GLN C 66 HIS C 125 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN B C1058 HIS B 394 ASN B1010 GLN B ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.110391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082717 restraints weight = 135124.537| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.30 r_work: 0.2706 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 36174 Z= 0.246 Angle : 0.822 19.918 49440 Z= 0.396 Chirality : 0.058 0.764 5847 Planarity : 0.006 0.156 6213 Dihedral : 5.975 44.734 4739 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.02 % Favored : 93.37 % Rotamer: Outliers : 0.85 % Allowed : 8.91 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.12), residues: 4395 helix: 0.78 (0.20), residues: 711 sheet: -0.19 (0.14), residues: 1368 loop : -1.30 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1039 TYR 0.025 0.002 TYR C1067 PHE 0.033 0.002 PHE C 906 TRP 0.037 0.002 TRP A 258 HIS 0.011 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (36036) covalent geometry : angle 0.76394 / 0.38 (49077) SS BOND : bond 0.00366 / 0.22 ( 51) SS BOND : angle 1.16961 / 0.75 ( 102) hydrogen bonds : bond 0.04716 / 3.16 ( 1291) hydrogen bonds : angle 6.06668 / 4.19 ( 3612) link_BETA1-3 : bond 0.01100 / 0.55 ( 2) link_BETA1-3 : angle 2.04083 / 0.91 ( 6) link_BETA1-4 : bond 0.00526 / 0.36 ( 31) link_BETA1-4 : angle 1.88835 / 1.27 ( 93) link_NAG-ASN : bond 0.01295 / 0.99 ( 54) link_NAG-ASN : angle 5.13450 / 3.24 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 370 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 TRP cc_start: 0.6168 (m-10) cc_final: 0.5592 (m-10) REVERT: E 73 TYR cc_start: 0.7730 (m-80) cc_final: 0.7468 (m-80) REVERT: D 117 ARG cc_start: 0.7301 (ttt90) cc_final: 0.6279 (ttt90) REVERT: D 196 PHE cc_start: 0.6431 (t80) cc_final: 0.6195 (t80) REVERT: L 60 TYR cc_start: 0.8332 (m-10) cc_final: 0.7950 (m-10) REVERT: H 100 MET cc_start: 0.8185 (tmm) cc_final: 0.7853 (tmm) REVERT: H 216 PHE cc_start: 0.5924 (m-80) cc_final: 0.5426 (m-80) REVERT: C 133 PHE cc_start: 0.8258 (m-10) cc_final: 0.7989 (m-10) REVERT: C 378 LYS cc_start: 0.8407 (tptm) cc_final: 0.8138 (tptm) REVERT: C 396 TYR cc_start: 0.8514 (m-80) cc_final: 0.8114 (m-80) REVERT: C 486 PHE cc_start: 0.8772 (m-10) cc_final: 0.8399 (m-80) REVERT: B 102 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8307 (mtt-85) REVERT: G 110 TYR cc_start: 0.8686 (m-80) cc_final: 0.8300 (m-80) REVERT: F 54 ASN cc_start: 0.8096 (t0) cc_final: 0.7710 (t0) REVERT: F 65 GLU cc_start: 0.8305 (tp30) cc_final: 0.8041 (tm-30) REVERT: F 67 ILE cc_start: 0.8536 (mm) cc_final: 0.7807 (mm) REVERT: F 121 ASP cc_start: 0.8464 (p0) cc_final: 0.8173 (p0) REVERT: F 250 HIS cc_start: 0.1474 (t-170) cc_final: -0.0119 (t-90) outliers start: 29 outliers final: 17 residues processed: 386 average time/residue: 0.1942 time to fit residues: 126.1710 Evaluate side-chains 358 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 340 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [260, 343, 341, 223, 122, 245, 100, 129, 362, 10, 37] chunk 260 optimal weight: 0.7980 chunk 343 optimal weight: 5.9990 chunk 341 optimal weight: 0.0470 chunk 223 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 362 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 GLN H 125 GLN C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.111340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083915 restraints weight = 145876.751| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.52 r_work: 0.2718 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 36174 Z= 0.151 Angle : 0.750 19.785 49440 Z= 0.358 Chirality : 0.054 0.612 5847 Planarity : 0.006 0.148 6213 Dihedral : 5.709 42.920 4739 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.20 % Favored : 94.16 % Rotamer: Outliers : 0.96 % Allowed : 10.57 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.12), residues: 4395 helix: 1.04 (0.20), residues: 716 sheet: -0.11 (0.14), residues: 1349 loop : -1.25 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 44 TYR 0.021 0.001 TYR E 73 PHE 0.028 0.002 PHE F 48 TRP 0.027 0.002 TRP F 55 HIS 0.007 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (36036) covalent geometry : angle 0.69694 / 0.35 (49077) SS BOND : bond 0.00247 / 0.16 ( 51) SS BOND : angle 0.93666 / 0.61 ( 102) hydrogen bonds : bond 0.03981 / 2.66 ( 1291) hydrogen bonds : angle 5.82273 / 4.02 ( 3612) link_BETA1-3 : bond 0.01151 / 0.57 ( 2) link_BETA1-3 : angle 1.81559 / 0.80 ( 6) link_BETA1-4 : bond 0.00561 / 0.38 ( 31) link_BETA1-4 : angle 1.70477 / 1.16 ( 93) link_NAG-ASN : bond 0.01215 / 0.92 ( 54) link_NAG-ASN : angle 4.72812 / 2.96 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 TRP cc_start: 0.6350 (m-10) cc_final: 0.5629 (m-10) REVERT: D 53 MET cc_start: 0.9004 (tpt) cc_final: 0.8751 (tpp) REVERT: D 79 ASP cc_start: 0.7616 (t0) cc_final: 0.7391 (t0) REVERT: D 117 ARG cc_start: 0.7229 (ttt90) cc_final: 0.6590 (ttt90) REVERT: D 196 PHE cc_start: 0.6477 (t80) cc_final: 0.6213 (t80) REVERT: L 60 TYR cc_start: 0.8293 (m-10) cc_final: 0.8006 (m-10) REVERT: H 56 MET cc_start: 0.8192 (mmm) cc_final: 0.7800 (mmm) REVERT: H 100 MET cc_start: 0.8136 (tmm) cc_final: 0.7819 (tmm) REVERT: H 125 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: H 216 PHE cc_start: 0.5988 (m-80) cc_final: 0.5500 (m-80) REVERT: C 378 LYS cc_start: 0.8482 (tptm) cc_final: 0.8259 (tptm) REVERT: C 396 TYR cc_start: 0.8547 (m-80) cc_final: 0.8121 (m-80) REVERT: C 486 PHE cc_start: 0.8735 (m-10) cc_final: 0.8442 (m-80) REVERT: B 102 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8251 (mtt-85) REVERT: B 380 TYR cc_start: 0.8825 (m-10) cc_final: 0.8592 (m-10) REVERT: F 54 ASN cc_start: 0.8099 (t0) cc_final: 0.7629 (t0) REVERT: F 56 MET cc_start: 0.8438 (mmm) cc_final: 0.8236 (mmm) REVERT: F 67 ILE cc_start: 0.8536 (mm) cc_final: 0.7980 (mm) REVERT: F 101 GLN cc_start: 0.7338 (tp-100) cc_final: 0.6938 (tp-100) REVERT: F 121 ASP cc_start: 0.8351 (p0) cc_final: 0.8092 (p0) outliers start: 33 outliers final: 21 residues processed: 394 average time/residue: 0.1933 time to fit residues: 127.8121 Evaluate side-chains 373 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 350 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 125 GLN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [258, 225, 255, 50, 410, 160, 233, 19, 57, 325, 42] chunk 258 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 410 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 GLN F 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.108600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080732 restraints weight = 132730.210| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.30 r_work: 0.2644 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.104 36174 Z= 0.416 Angle : 0.947 25.218 49440 Z= 0.459 Chirality : 0.064 0.542 5847 Planarity : 0.007 0.180 6213 Dihedral : 6.311 48.772 4739 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.02 % Favored : 92.36 % Rotamer: Outliers : 1.63 % Allowed : 11.32 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4395 helix: 0.33 (0.19), residues: 723 sheet: -0.26 (0.13), residues: 1406 loop : -1.37 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1039 TYR 0.031 0.003 TYR C1067 PHE 0.035 0.003 PHE F 48 TRP 0.028 0.003 TRP F 55 HIS 0.028 0.002 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00996 / 0.42 (36036) covalent geometry : angle 0.89456 / 0.45 (49077) SS BOND : bond 0.00482 / 0.32 ( 51) SS BOND : angle 1.13904 / 0.77 ( 102) hydrogen bonds : bond 0.05392 / 3.60 ( 1291) hydrogen bonds : angle 6.18338 / 4.25 ( 3612) link_BETA1-3 : bond 0.01022 / 0.52 ( 2) link_BETA1-3 : angle 2.35368 / 1.18 ( 6) link_BETA1-4 : bond 0.00495 / 0.34 ( 31) link_BETA1-4 : angle 2.25436 / 1.49 ( 93) link_NAG-ASN : bond 0.01287 / 0.96 ( 54) link_NAG-ASN : angle 5.23529 / 3.32 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 371 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 TRP cc_start: 0.6892 (m-10) cc_final: 0.6522 (m-10) REVERT: A 410 ILE cc_start: 0.9517 (mm) cc_final: 0.9275 (mt) REVERT: A 471 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7523 (pm20) REVERT: A 474 GLN cc_start: 0.8257 (tp40) cc_final: 0.8019 (tp40) REVERT: D 53 MET cc_start: 0.8921 (tpt) cc_final: 0.8681 (tpp) REVERT: D 100 MET cc_start: 0.8569 (tmm) cc_final: 0.7738 (tmm) REVERT: D 117 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7072 (ttt180) REVERT: H 56 MET cc_start: 0.8091 (mmm) cc_final: 0.7612 (mmm) REVERT: H 100 MET cc_start: 0.8274 (tmm) cc_final: 0.7843 (tmm) REVERT: H 125 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: H 216 PHE cc_start: 0.6180 (m-80) cc_final: 0.5972 (m-10) REVERT: C 378 LYS cc_start: 0.8455 (tptm) cc_final: 0.8204 (tptm) REVERT: C 387 LEU cc_start: 0.8571 (mt) cc_final: 0.8206 (mt) REVERT: C 455 LEU cc_start: 0.9004 (mp) cc_final: 0.8737 (mp) REVERT: C 486 PHE cc_start: 0.8847 (m-10) cc_final: 0.8642 (m-10) REVERT: B 18 LEU cc_start: 0.8750 (tp) cc_final: 0.8483 (tp) REVERT: B 164 ASN cc_start: 0.8006 (p0) cc_final: 0.7620 (p0) REVERT: G 70 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8198 (t) REVERT: F 46 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.4634 (t80) REVERT: F 56 MET cc_start: 0.8314 (mmm) cc_final: 0.8095 (mmm) REVERT: F 101 GLN cc_start: 0.7416 (tp-100) cc_final: 0.7077 (tp-100) REVERT: F 115 CYS cc_start: 0.5606 (p) cc_final: 0.5305 (p) REVERT: F 250 HIS cc_start: 0.1943 (t-170) cc_final: 0.0057 (t-90) outliers start: 58 outliers final: 37 residues processed: 403 average time/residue: 0.1909 time to fit residues: 130.2253 Evaluate side-chains 384 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 125 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [108, 242, 36, 279, 164, 291, 14, 154, 123, 286, 159] chunk 108 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 164 optimal weight: 30.0000 chunk 291 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 394 ASN B 409 GLN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 25 GLN ** 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 = 0.3945 r_free = 0.3945 target = 0.109816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.086924 restraints weight = 172509.249| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.80 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36174 Z= 0.202 Angle : 0.798 19.886 49440 Z= 0.381 Chirality : 0.055 0.535 5847 Planarity : 0.006 0.159 6213 Dihedral : 6.024 44.877 4739 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.49 % Favored : 93.94 % Rotamer: Outliers : 1.55 % Allowed : 12.04 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.12), residues: 4395 helix: 0.80 (0.20), residues: 715 sheet: -0.23 (0.13), residues: 1377 loop : -1.30 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 102 TYR 0.025 0.002 TYR E 73 PHE 0.029 0.002 PHE F 48 TRP 0.051 0.002 TRP B 258 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (36036) covalent geometry : angle 0.74816 / 0.37 (49077) SS BOND : bond 0.00285 / 0.18 ( 51) SS BOND : angle 0.97396 / 0.65 ( 102) hydrogen bonds : bond 0.04321 / 2.89 ( 1291) hydrogen bonds : angle 5.88644 / 4.06 ( 3612) link_BETA1-3 : bond 0.01050 / 0.53 ( 2) link_BETA1-3 : angle 1.79516 / 0.85 ( 6) link_BETA1-4 : bond 0.00559 / 0.37 ( 31) link_BETA1-4 : angle 1.81505 / 1.22 ( 93) link_NAG-ASN : bond 0.01211 / 0.92 ( 54) link_NAG-ASN : angle 4.70634 / 2.94 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLN cc_start: 0.7788 (tp40) cc_final: 0.7582 (tp40) REVERT: D 117 ARG cc_start: 0.6501 (ttt90) cc_final: 0.6300 (ttt180) REVERT: G 70 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7870 (t) REVERT: G 190 PHE cc_start: 0.3981 (p90) cc_final: 0.3031 (p90) REVERT: F 101 GLN cc_start: 0.6159 (tp-100) cc_final: 0.5950 (tp-100) REVERT: F 250 HIS cc_start: 0.0181 (t-170) cc_final: -0.0889 (t-90) outliers start: 55 outliers final: 38 residues processed: 391 average time/residue: 0.1831 time to fit residues: 121.9223 Evaluate side-chains 381 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 342 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [209, 177, 138, 30, 393, 162, 110, 105, 415, 367, 172] chunk 209 optimal weight: 0.0980 chunk 177 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 393 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 105 optimal weight: 0.0570 chunk 415 optimal weight: 20.0000 chunk 367 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 GLN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.110653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.084932 restraints weight = 161450.748| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.85 r_work: 0.2696 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 36174 Z= 0.151 Angle : 0.760 19.629 49440 Z= 0.362 Chirality : 0.053 0.495 5847 Planarity : 0.006 0.149 6213 Dihedral : 5.758 42.232 4739 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.86 % Favored : 93.57 % Rotamer: Outliers : 1.31 % Allowed : 12.54 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.12), residues: 4395 helix: 1.12 (0.20), residues: 721 sheet: -0.19 (0.13), residues: 1387 loop : -1.29 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 117 TYR 0.026 0.001 TYR E 73 PHE 0.032 0.002 PHE A 133 TRP 0.038 0.002 TRP F 55 HIS 0.016 0.001 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (36036) covalent geometry : angle 0.71427 / 0.35 (49077) SS BOND : bond 0.00279 / 0.15 ( 51) SS BOND : angle 0.89428 / 0.60 ( 102) hydrogen bonds : bond 0.03889 / 2.61 ( 1291) hydrogen bonds : angle 5.70596 / 3.94 ( 3612) link_BETA1-3 : bond 0.01052 / 0.53 ( 2) link_BETA1-3 : angle 1.52189 / 0.70 ( 6) link_BETA1-4 : bond 0.00537 / 0.36 ( 31) link_BETA1-4 : angle 1.70578 / 1.16 ( 93) link_NAG-ASN : bond 0.01175 / 0.90 ( 54) link_NAG-ASN : angle 4.41678 / 2.75 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9060 (m-40) cc_final: 0.8458 (p0) REVERT: A 474 GLN cc_start: 0.8369 (tp40) cc_final: 0.8097 (tp40) REVERT: D 29 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7841 (mm-30) REVERT: D 55 TRP cc_start: 0.7881 (m100) cc_final: 0.7624 (m100) REVERT: D 100 MET cc_start: 0.8610 (tmm) cc_final: 0.7785 (tmm) REVERT: D 194 ASP cc_start: 0.7569 (m-30) cc_final: 0.7255 (m-30) REVERT: L 106 ASP cc_start: 0.7133 (m-30) cc_final: 0.6904 (m-30) REVERT: H 24 GLN cc_start: 0.6974 (mp10) cc_final: 0.6744 (mp10) REVERT: H 125 GLN cc_start: 0.7869 (pm20) cc_final: 0.7638 (pm20) REVERT: H 216 PHE cc_start: 0.6016 (m-10) cc_final: 0.5790 (m-80) REVERT: C 338 PHE cc_start: 0.8741 (m-80) cc_final: 0.8375 (m-80) REVERT: B 452 LEU cc_start: 0.9082 (pt) cc_final: 0.8864 (pp) REVERT: G 190 PHE cc_start: 0.6512 (p90) cc_final: 0.5458 (p90) REVERT: F 46 TYR cc_start: 0.5440 (OUTLIER) cc_final: 0.5013 (t80) REVERT: F 101 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6848 (tp40) REVERT: F 204 TRP cc_start: 0.4777 (m100) cc_final: 0.4339 (m100) outliers start: 46 outliers final: 35 residues processed: 393 average time/residue: 0.1877 time to fit residues: 124.8164 Evaluate side-chains 381 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 345 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [422, 369, 67, 246, 342, 426, 131, 102, 371, 372, 358] chunk 422 optimal weight: 8.9990 chunk 369 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 342 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 371 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 358 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.110782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083210 restraints weight = 138628.538| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 4.49 r_work: 0.2724 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 36174 Z= 0.155 Angle : 0.757 19.450 49440 Z= 0.362 Chirality : 0.053 0.474 5847 Planarity : 0.006 0.147 6213 Dihedral : 5.690 42.067 4739 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.79 % Favored : 93.64 % Rotamer: Outliers : 1.33 % Allowed : 12.62 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4395 helix: 1.22 (0.20), residues: 721 sheet: -0.16 (0.14), residues: 1387 loop : -1.26 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 117 TYR 0.051 0.002 TYR E 191 PHE 0.021 0.002 PHE C 133 TRP 0.044 0.002 TRP F 55 HIS 0.007 0.001 HIS F 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (36036) covalent geometry : angle 0.71235 / 0.35 (49077) SS BOND : bond 0.00275 / 0.18 ( 51) SS BOND : angle 0.91397 / 0.62 ( 102) hydrogen bonds : bond 0.03871 / 2.60 ( 1291) hydrogen bonds : angle 5.62906 / 3.89 ( 3612) link_BETA1-3 : bond 0.00984 / 0.50 ( 2) link_BETA1-3 : angle 1.49108 / 0.69 ( 6) link_BETA1-4 : bond 0.00534 / 0.36 ( 31) link_BETA1-4 : angle 1.69765 / 1.16 ( 93) link_NAG-ASN : bond 0.01191 / 0.91 ( 54) link_NAG-ASN : angle 4.36337 / 2.72 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 359 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9051 (m-40) cc_final: 0.8460 (p0) REVERT: A 153 MET cc_start: 0.7620 (mmp) cc_final: 0.7193 (ptp) REVERT: A 231 ILE cc_start: 0.9325 (mp) cc_final: 0.8817 (mm) REVERT: A 474 GLN cc_start: 0.8340 (tp40) cc_final: 0.8069 (tp40) REVERT: D 29 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7714 (mm-30) REVERT: D 55 TRP cc_start: 0.7910 (m100) cc_final: 0.7685 (m100) REVERT: D 79 ASP cc_start: 0.7673 (t0) cc_final: 0.7291 (t0) REVERT: L 73 TYR cc_start: 0.8111 (m-80) cc_final: 0.7897 (m-80) REVERT: L 106 ASP cc_start: 0.7099 (m-30) cc_final: 0.6861 (m-30) REVERT: H 24 GLN cc_start: 0.6921 (mp10) cc_final: 0.6710 (mp10) REVERT: H 100 MET cc_start: 0.7783 (tmm) cc_final: 0.7268 (tmm) REVERT: H 123 TRP cc_start: 0.8533 (m-10) cc_final: 0.8188 (m-10) REVERT: H 125 GLN cc_start: 0.7726 (pm20) cc_final: 0.7448 (pm20) REVERT: H 216 PHE cc_start: 0.6065 (m-10) cc_final: 0.5749 (m-80) REVERT: C 493 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8089 (pp30) REVERT: B 452 LEU cc_start: 0.9103 (pt) cc_final: 0.8843 (pp) REVERT: B 595 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8736 (t) REVERT: G 190 PHE cc_start: 0.6331 (p90) cc_final: 0.5341 (p90) REVERT: F 46 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.5057 (t80) REVERT: F 71 ASN cc_start: 0.7614 (t0) cc_final: 0.7246 (t0) REVERT: F 101 GLN cc_start: 0.7338 (tp-100) cc_final: 0.6898 (tp40) REVERT: F 119 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8210 (mtm-85) outliers start: 47 outliers final: 39 residues processed: 388 average time/residue: 0.1785 time to fit residues: 117.5979 Evaluate side-chains 387 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 346 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [297, 147, 3, 200, 123, 83, 317, 5, 67, 186, 360] chunk 297 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 360 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.109665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085199 restraints weight = 155323.358| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.46 r_work: 0.2662 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 36174 Z= 0.238 Angle : 0.807 19.454 49440 Z= 0.389 Chirality : 0.055 0.477 5847 Planarity : 0.006 0.149 6213 Dihedral : 5.879 44.588 4739 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.38 % Favored : 93.02 % Rotamer: Outliers : 1.28 % Allowed : 12.92 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.12), residues: 4395 helix: 1.01 (0.20), residues: 715 sheet: -0.21 (0.14), residues: 1395 loop : -1.26 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 117 TYR 0.050 0.002 TYR E 191 PHE 0.021 0.002 PHE L 111 TRP 0.030 0.002 TRP F 55 HIS 0.009 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (36036) covalent geometry : angle 0.76127 / 0.38 (49077) SS BOND : bond 0.00326 / 0.22 ( 51) SS BOND : angle 0.96775 / 0.65 ( 102) hydrogen bonds : bond 0.04423 / 2.97 ( 1291) hydrogen bonds : angle 5.76335 / 3.98 ( 3612) link_BETA1-3 : bond 0.00968 / 0.49 ( 2) link_BETA1-3 : angle 1.65827 / 0.81 ( 6) link_BETA1-4 : bond 0.00483 / 0.31 ( 31) link_BETA1-4 : angle 1.85366 / 1.24 ( 93) link_NAG-ASN : bond 0.01161 / 0.88 ( 54) link_NAG-ASN : angle 4.54085 / 2.85 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 356 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9071 (m-40) cc_final: 0.8487 (p0) REVERT: A 153 MET cc_start: 0.7717 (mmp) cc_final: 0.7316 (ptp) REVERT: D 55 TRP cc_start: 0.8029 (m100) cc_final: 0.7781 (m100) REVERT: D 79 ASP cc_start: 0.7608 (t0) cc_final: 0.7220 (t0) REVERT: L 73 TYR cc_start: 0.8172 (m-80) cc_final: 0.7943 (m-80) REVERT: L 106 ASP cc_start: 0.7021 (m-30) cc_final: 0.6795 (m-30) REVERT: H 24 GLN cc_start: 0.6967 (mp10) cc_final: 0.6759 (mp10) REVERT: H 100 MET cc_start: 0.7845 (tmm) cc_final: 0.7238 (tmm) REVERT: H 123 TRP cc_start: 0.8550 (m-10) cc_final: 0.8216 (m-10) REVERT: H 125 GLN cc_start: 0.7916 (pm20) cc_final: 0.7632 (pm20) REVERT: H 216 PHE cc_start: 0.6176 (m-10) cc_final: 0.5862 (m-80) REVERT: C 387 LEU cc_start: 0.8488 (mt) cc_final: 0.8129 (mt) REVERT: B 164 ASN cc_start: 0.7828 (p0) cc_final: 0.7498 (p0) REVERT: B 380 TYR cc_start: 0.8776 (m-10) cc_final: 0.8459 (m-10) REVERT: B 595 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8734 (t) REVERT: G 190 PHE cc_start: 0.6370 (p90) cc_final: 0.5327 (p90) REVERT: F 46 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.5306 (t80) REVERT: F 58 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8048 (tp40) REVERT: F 71 ASN cc_start: 0.7724 (t0) cc_final: 0.7328 (t0) REVERT: F 101 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6701 (tp40) REVERT: F 119 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7845 (mtm-85) REVERT: F 204 TRP cc_start: 0.4626 (m100) cc_final: 0.4043 (m100) outliers start: 45 outliers final: 39 residues processed: 382 average time/residue: 0.1806 time to fit residues: 117.3490 Evaluate side-chains 390 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [375, 268, 61, 179, 354, 213, 422, 327, 104, 224, 355] chunk 375 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 354 optimal weight: 0.6980 chunk 213 optimal weight: 0.9990 chunk 422 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 355 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 146 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 394 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.110700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083676 restraints weight = 149834.077| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.73 r_work: 0.2710 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36174 Z= 0.149 Angle : 0.753 19.254 49440 Z= 0.360 Chirality : 0.052 0.461 5847 Planarity : 0.006 0.149 6213 Dihedral : 5.679 42.359 4739 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.52 % Favored : 93.89 % Rotamer: Outliers : 1.17 % Allowed : 13.13 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4395 helix: 1.28 (0.20), residues: 708 sheet: -0.18 (0.14), residues: 1387 loop : -1.24 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.027 0.001 TYR E 191 PHE 0.020 0.001 PHE A 140 TRP 0.039 0.002 TRP A 258 HIS 0.005 0.001 HIS F 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (36036) covalent geometry : angle 0.70927 / 0.35 (49077) SS BOND : bond 0.00286 / 0.18 ( 51) SS BOND : angle 0.97780 / 0.63 ( 102) hydrogen bonds : bond 0.03863 / 2.59 ( 1291) hydrogen bonds : angle 5.61531 / 3.88 ( 3612) link_BETA1-3 : bond 0.00971 / 0.49 ( 2) link_BETA1-3 : angle 1.42154 / 0.67 ( 6) link_BETA1-4 : bond 0.00531 / 0.36 ( 31) link_BETA1-4 : angle 1.67061 / 1.14 ( 93) link_NAG-ASN : bond 0.01156 / 0.88 ( 54) link_NAG-ASN : angle 4.30297 / 2.68 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8790 Ramachandran restraints generated. 4395 Oldfield, 0 Emsley, 4395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9303 (mm) cc_final: 0.9085 (mm) REVERT: A 137 ASN cc_start: 0.9086 (m-40) cc_final: 0.8421 (p0) REVERT: A 153 MET cc_start: 0.7643 (mmp) cc_final: 0.7257 (ptp) REVERT: D 55 TRP cc_start: 0.7962 (m100) cc_final: 0.7694 (m100) REVERT: D 79 ASP cc_start: 0.7615 (t0) cc_final: 0.7244 (t0) REVERT: L 73 TYR cc_start: 0.8106 (m-80) cc_final: 0.7900 (m-80) REVERT: L 106 ASP cc_start: 0.6956 (m-30) cc_final: 0.6720 (m-30) REVERT: H 65 GLU cc_start: 0.7792 (pm20) cc_final: 0.7589 (pm20) REVERT: H 100 MET cc_start: 0.7958 (tmm) cc_final: 0.7356 (tmm) REVERT: H 123 TRP cc_start: 0.8662 (m-10) cc_final: 0.8339 (m-10) REVERT: H 125 GLN cc_start: 0.7848 (pm20) cc_final: 0.7556 (pm20) REVERT: H 216 PHE cc_start: 0.6180 (m-10) cc_final: 0.5821 (m-80) REVERT: C 387 LEU cc_start: 0.8497 (mt) cc_final: 0.8121 (mt) REVERT: B 380 TYR cc_start: 0.8786 (m-10) cc_final: 0.8514 (m-10) REVERT: B 452 LEU cc_start: 0.9101 (pt) cc_final: 0.8826 (pp) REVERT: B 595 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8745 (t) REVERT: G 190 PHE cc_start: 0.6411 (p90) cc_final: 0.5398 (p90) REVERT: F 71 ASN cc_start: 0.7571 (t0) cc_final: 0.7161 (t0) REVERT: F 101 GLN cc_start: 0.7403 (tp-100) cc_final: 0.6857 (tp40) REVERT: F 117 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7613 (ttp80) REVERT: F 204 TRP cc_start: 0.4649 (m100) cc_final: 0.4031 (m100) outliers start: 41 outliers final: 36 residues processed: 378 average time/residue: 0.1762 time to fit residues: 113.1794 Evaluate side-chains 383 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 346 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [268, 150, 3, 405, 402, 47, 254, 80, 81, 74, 82] chunk 268 optimal weight: 0.8980 chunk 150 optimal weight: 0.0370 chunk 3 optimal weight: 0.4980 chunk 405 optimal weight: 0.9990 chunk 402 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.111348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086547 restraints weight = 157584.120| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.62 r_work: 0.2727 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36174 Z= 0.131 Angle : 0.732 19.170 49440 Z= 0.350 Chirality : 0.051 0.439 5847 Planarity : 0.006 0.149 6213 Dihedral : 5.497 40.893 4739 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.86 % Favored : 93.55 % Rotamer: Outliers : 1.20 % Allowed : 13.16 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4395 helix: 1.49 (0.20), residues: 708 sheet: -0.14 (0.14), residues: 1386 loop : -1.23 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 117 TYR 0.038 0.001 TYR F 46 PHE 0.021 0.001 PHE G 111 TRP 0.047 0.002 TRP F 55 HIS 0.016 0.001 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (36036) covalent geometry : angle 0.69002 / 0.34 (49077) SS BOND : bond 0.00215 / 0.14 ( 51) SS BOND : angle 0.86325 / 0.57 ( 102) hydrogen bonds : bond 0.03584 / 2.41 ( 1291) hydrogen bonds : angle 5.48743 / 3.79 ( 3612) link_BETA1-3 : bond 0.00781 / 0.39 ( 2) link_BETA1-3 : angle 1.24773 / 0.57 ( 6) link_BETA1-4 : bond 0.00563 / 0.38 ( 31) link_BETA1-4 : angle 1.60868 / 1.10 ( 93) link_NAG-ASN : bond 0.01128 / 0.85 ( 54) link_NAG-ASN : angle 4.14724 / 2.58 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9735.98 seconds wall clock time: 167 minutes 13.15 seconds (10033.15 seconds total)