Starting phenix.real_space_refine on Thu Oct 29 20:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mw2_24060/10_2026/7mw2_24060.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21459 2.51 5 N 5529 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33807 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7745 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7902 Chain: "G" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 Time building chain proxies: 10.61, per 1000 atoms: 0.31 Number of scatterers: 33807 At special positions: 0 Unit cell: (138.84, 140.976, 222.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 6672 8.00 N 5529 7.00 C 21459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 158 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 164 " - pdb=" SG CYS F 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 125 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 125 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1074 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 234 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B 709 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 343 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8028 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 79 sheets defined 20.6% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.061A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.597A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.692A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.217A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.566A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.713A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.890A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.742A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.072A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.625A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.789A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.240A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.709A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.558A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.251A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.586A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.818A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.793A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'L' and resid 207 through 211 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 211 through 214 removed outlier: 4.295A pdb=" N GLY H 214 " --> pdb=" O SER H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.026A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.751A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.754A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.720A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.106A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.647A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.744A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.207A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.509A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.884A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.849A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 211 through 214 removed outlier: 4.188A pdb=" N GLY F 214 " --> pdb=" O SER F 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.700A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.220A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.188A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.965A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 319 removed outlier: 5.767A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.733A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.878A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.532A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.164A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'E' and resid 24 through 27 Processing sheet with id=AC2, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.386A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.386A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 121 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 138 through 142 removed outlier: 6.080A pdb=" N TYR E 197 " --> pdb=" O ASN E 162 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER E 198 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AC6, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.003A pdb=" N ALA D 125 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY D 119 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TRP D 127 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG D 117 " --> pdb=" O TRP D 127 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN D 129 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 115 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.030A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.030A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.254A pdb=" N TYR D 218 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.822A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.036A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.363A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.993A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 312 through 319 removed outlier: 6.030A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.239A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.751A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.561A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.152A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.286A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.286A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AF4, first strand: chain 'L' and resid 138 through 142 removed outlier: 5.948A pdb=" N TYR L 197 " --> pdb=" O ASN L 162 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER L 198 " --> pdb=" O THR L 188 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 177 through 178 Processing sheet with id=AF6, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AF7, first strand: chain 'H' and resid 29 through 31 removed outlier: 4.995A pdb=" N ALA H 125 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY H 119 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TRP H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG H 117 " --> pdb=" O TRP H 127 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN H 129 " --> pdb=" O CYS H 115 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS H 115 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.066A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.066A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 175 through 178 removed outlier: 4.172A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.781A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AG4, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.053A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.356A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.849A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 312 through 319 removed outlier: 5.925A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.693A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AG9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AH2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.377A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.377A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.186A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AH7, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH8, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.263A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.263A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 138 through 142 removed outlier: 6.070A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 198 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 168 through 174 Processing sheet with id=AI3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AI4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.993A pdb=" N ALA F 125 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY F 119 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TRP F 127 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG F 117 " --> pdb=" O TRP F 127 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN F 129 " --> pdb=" O CYS F 115 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS F 115 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR F 69 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.126A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.126A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 175 through 178 removed outlier: 4.218A pdb=" N TYR F 218 " --> pdb=" O VAL F 235 " (cutoff:3.500A) 1495 hydrogen bonds defined for protein. 4056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.22 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9292 1.33 - 1.46: 7322 1.46 - 1.58: 17766 1.58 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 34569 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 34564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 46132 2.12 - 4.24: 897 4.24 - 6.36: 78 6.36 - 8.48: 10 8.48 - 10.60: 4 Bond angle restraints: 47121 Sorted by residual: angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 111.77 103.74 8.03 1.04e+00 9.25e-01 5.96e+01 angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.77 104.57 7.20 1.04e+00 9.25e-01 4.79e+01 angle pdb=" N GLY C 502 " pdb=" CA GLY C 502 " pdb=" C GLY C 502 " ideal model delta sigma weight residual 111.93 106.87 5.06 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N GLY A 502 " pdb=" CA GLY A 502 " pdb=" C GLY A 502 " ideal model delta sigma weight residual 111.93 107.12 4.81 1.15e+00 7.56e-01 1.75e+01 angle pdb=" C GLN A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.85 115.66 4.19 1.01e+00 9.80e-01 1.72e+01 ... (remaining 47116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18533 17.98 - 35.97: 1147 35.97 - 53.95: 221 53.95 - 71.93: 41 71.93 - 89.92: 20 Dihedral angle restraints: 19962 sinusoidal: 7473 harmonic: 12489 Sorted by residual: dihedral pdb=" CA SER L 27 " pdb=" C SER L 27 " pdb=" N PRO L 28 " pdb=" CA PRO L 28 " ideal model delta harmonic sigma weight residual -180.00 -108.14 -71.86 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CA SER G 27 " pdb=" C SER G 27 " pdb=" N PRO G 28 " pdb=" CA PRO G 28 " ideal model delta harmonic sigma weight residual -180.00 -108.16 -71.84 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" CA SER E 27 " pdb=" C SER E 27 " pdb=" N PRO E 28 " pdb=" CA PRO E 28 " ideal model delta harmonic sigma weight residual -180.00 -108.38 -71.62 0 5.00e+00 4.00e-02 2.05e+02 ... (remaining 19959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.540: 5586 0.540 - 1.080: 3 1.080 - 1.620: 0 1.620 - 2.161: 2 2.161 - 2.701: 4 Chirality restraints: 5595 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 0.30 -2.70 2.00e-01 2.50e+01 1.82e+02 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 0.25 -2.65 2.00e-01 2.50e+01 1.76e+02 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 0.24 -2.64 2.00e-01 2.50e+01 1.74e+02 ... (remaining 5592 not shown) Planarity restraints: 6054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " 0.249 2.00e-02 2.50e+03 2.12e-01 5.61e+02 pdb=" C7 NAG A1309 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " -0.363 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.245 2.00e-02 2.50e+03 2.08e-01 5.40e+02 pdb=" C7 NAG B1309 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.217 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG C1310 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.291 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " -0.022 2.00e-02 2.50e+03 ... (remaining 6051 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1837 2.73 - 3.27: 32793 3.27 - 3.82: 55951 3.82 - 4.36: 69590 4.36 - 4.90: 119210 Nonbonded interactions: 279381 Sorted by model distance: nonbonded pdb=" OG SER C 591 " pdb=" OE2 GLU C 619 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.295 3.040 nonbonded pdb=" ND2 ASN D 221 " pdb=" OD1 ASP D 232 " model vdw 2.299 3.120 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR A 859 " pdb=" OD2 ASP B 614 " model vdw 2.324 3.040 ... (remaining 279376 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1310)) selection = (chain 'B' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1310)) selection = (chain 'C' and (resid 27 through 465 or resid 467 through 1009 or resid 1011 thr \ ough 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 39.100 Find NCS groups from input model: 1.030 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 0.131 34692 Z= 0.231 Angle : 0.883 46.871 47439 Z= 0.415 Chirality : 0.094 2.701 5595 Planarity : 0.007 0.212 6003 Dihedral : 12.477 89.917 11781 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 4233 helix: 0.52 (0.19), residues: 729 sheet: 0.56 (0.14), residues: 1323 loop : -0.83 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 44 TYR 0.019 0.001 TYR E 73 PHE 0.024 0.002 PHE A 906 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 (34569) covalent geometry : angle 0.68439 / 0.37 (47121) SS BOND : bond 0.00247 / 0.16 ( 51) SS BOND : angle 1.34197 / 0.85 ( 102) hydrogen bonds : bond 0.16399 / 11.02 ( 1400) hydrogen bonds : angle 7.71953 / 5.43 ( 4056) link_BETA1-4 : bond 0.00672 / 0.43 ( 21) link_BETA1-4 : angle 3.71584 / 2.29 ( 63) link_NAG-ASN : bond 0.04190 / 1.72 ( 51) link_NAG-ASN : angle 9.52349 / 6.70 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 MET cc_start: 0.7623 (tpt) cc_final: 0.7351 (tpp) REVERT: H 146 PHE cc_start: 0.6965 (m-10) cc_final: 0.6685 (m-10) REVERT: B 697 MET cc_start: 0.8578 (ptm) cc_final: 0.8226 (ptm) outliers start: 3 outliers final: 4 residues processed: 307 average time/residue: 0.6518 time to fit residues: 243.0675 Evaluate side-chains 231 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 424, 155] chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS C 901 GLN C1010 GLN A ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 901 GLN ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.065220 restraints weight = 118315.972| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.96 r_work: 0.2804 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34692 Z= 0.213 Angle : 0.769 18.382 47439 Z= 0.358 Chirality : 0.057 0.790 5595 Planarity : 0.005 0.065 6003 Dihedral : 5.181 71.358 4589 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.61 % Rotamer: Outliers : 1.70 % Allowed : 4.98 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4233 helix: 1.31 (0.20), residues: 702 sheet: 0.50 (0.14), residues: 1344 loop : -0.95 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 44 TYR 0.026 0.002 TYR B1067 PHE 0.038 0.002 PHE C 906 TRP 0.020 0.002 TRP C 886 HIS 0.007 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (34569) covalent geometry : angle 0.68584 / 0.34 (47121) SS BOND : bond 0.00270 / 0.18 ( 51) SS BOND : angle 1.58336 / 1.02 ( 102) hydrogen bonds : bond 0.05083 / 3.38 ( 1400) hydrogen bonds : angle 6.11179 / 4.28 ( 4056) link_BETA1-4 : bond 0.00274 / 0.17 ( 21) link_BETA1-4 : angle 2.25305 / 1.41 ( 63) link_NAG-ASN : bond 0.01624 / 0.84 ( 51) link_NAG-ASN : angle 5.87613 / 3.97 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 101 GLN cc_start: 0.7631 (tp-100) cc_final: 0.6971 (tp40) REVERT: D 224 HIS cc_start: 0.4875 (t-170) cc_final: 0.4672 (t70) REVERT: C 904 TYR cc_start: 0.8363 (m-10) cc_final: 0.8013 (m-10) REVERT: L 103 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7339 (mm-30) REVERT: L 219 GLU cc_start: 0.6454 (tp30) cc_final: 0.6243 (tp30) REVERT: H 146 PHE cc_start: 0.7415 (m-10) cc_final: 0.7119 (m-10) REVERT: B 314 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8540 (tm-30) REVERT: F 101 GLN cc_start: 0.8127 (tt0) cc_final: 0.7772 (tt0) REVERT: F 225 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7392 (tppp) outliers start: 58 outliers final: 27 residues processed: 280 average time/residue: 0.6507 time to fit residues: 221.0699 Evaluate side-chains 261 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [336, 225, 246, 239, 203, 327, 160, 85, 126, 31, 257] chunk 336 optimal weight: 3.9990 chunk 225 optimal weight: 0.0870 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 327 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 957 GLN A1010 GLN A A1011 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.096219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.065860 restraints weight = 136168.753| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.16 r_work: 0.2811 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34692 Z= 0.144 Angle : 0.719 17.273 47439 Z= 0.331 Chirality : 0.054 0.704 5595 Planarity : 0.005 0.062 6003 Dihedral : 4.883 70.444 4585 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.06 % Favored : 96.73 % Rotamer: Outliers : 1.70 % Allowed : 6.34 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4233 helix: 1.69 (0.20), residues: 705 sheet: 0.45 (0.14), residues: 1344 loop : -0.95 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 44 TYR 0.022 0.001 TYR B 160 PHE 0.030 0.002 PHE C 133 TRP 0.014 0.001 TRP H 178 HIS 0.004 0.001 HIS H 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (34569) covalent geometry : angle 0.63618 / 0.31 (47121) SS BOND : bond 0.00425 / 0.29 ( 51) SS BOND : angle 1.65289 / 1.02 ( 102) hydrogen bonds : bond 0.04273 / 2.85 ( 1400) hydrogen bonds : angle 5.77144 / 4.03 ( 4056) link_BETA1-4 : bond 0.00303 / 0.17 ( 21) link_BETA1-4 : angle 2.18291 / 1.36 ( 63) link_NAG-ASN : bond 0.01564 / 0.85 ( 51) link_NAG-ASN : angle 5.64325 / 3.75 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 172 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8286 (mm-30) REVERT: D 224 HIS cc_start: 0.5064 (t-170) cc_final: 0.4637 (t70) REVERT: C 133 PHE cc_start: 0.8149 (m-80) cc_final: 0.7830 (m-80) REVERT: L 103 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7329 (mm-30) REVERT: L 219 GLU cc_start: 0.6484 (tp30) cc_final: 0.6178 (tp30) REVERT: H 146 PHE cc_start: 0.7388 (m-10) cc_final: 0.7117 (m-10) REVERT: F 101 GLN cc_start: 0.8044 (tt0) cc_final: 0.7654 (tt0) REVERT: F 146 PHE cc_start: 0.7283 (m-10) cc_final: 0.7009 (m-10) REVERT: F 225 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7292 (tppp) outliers start: 58 outliers final: 26 residues processed: 272 average time/residue: 0.6205 time to fit residues: 205.4687 Evaluate side-chains 250 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [326, 16, 355, 96, 225, 336, 80, 341, 305, 197, 235] chunk 326 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 355 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 134 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.064480 restraints weight = 138117.090| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.14 r_work: 0.2781 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34692 Z= 0.192 Angle : 0.733 16.537 47439 Z= 0.342 Chirality : 0.054 0.691 5595 Planarity : 0.005 0.063 6003 Dihedral : 5.046 70.188 4585 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 1.64 % Allowed : 7.67 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4233 helix: 1.74 (0.20), residues: 705 sheet: 0.42 (0.14), residues: 1344 loop : -0.98 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 44 TYR 0.029 0.001 TYR C 904 PHE 0.026 0.002 PHE B 133 TRP 0.024 0.001 TRP H 178 HIS 0.003 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (34569) covalent geometry : angle 0.66134 / 0.32 (47121) SS BOND : bond 0.00278 / 0.19 ( 51) SS BOND : angle 1.81465 / 1.15 ( 102) hydrogen bonds : bond 0.04402 / 2.94 ( 1400) hydrogen bonds : angle 5.72115 / 4.00 ( 4056) link_BETA1-4 : bond 0.00237 / 0.14 ( 21) link_BETA1-4 : angle 2.11341 / 1.32 ( 63) link_NAG-ASN : bond 0.01566 / 0.83 ( 51) link_NAG-ASN : angle 5.28783 / 3.46 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7850 (tp40) REVERT: D 101 GLN cc_start: 0.7436 (tp-100) cc_final: 0.6688 (tp-100) REVERT: D 172 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8364 (mm-30) REVERT: D 224 HIS cc_start: 0.5201 (t-170) cc_final: 0.4862 (t70) REVERT: C 603 ASN cc_start: 0.7113 (m110) cc_final: 0.6473 (p0) REVERT: C 619 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: L 44 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8034 (mtp85) REVERT: L 103 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7281 (mm-30) REVERT: L 142 PHE cc_start: 0.3496 (m-80) cc_final: 0.2872 (m-10) REVERT: L 219 GLU cc_start: 0.6642 (tp30) cc_final: 0.6280 (tp30) REVERT: H 146 PHE cc_start: 0.7387 (m-80) cc_final: 0.7021 (m-10) REVERT: B 166 CYS cc_start: 0.6118 (p) cc_final: 0.5883 (p) REVERT: B 314 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: F 101 GLN cc_start: 0.8108 (tt0) cc_final: 0.7825 (tt0) REVERT: F 146 PHE cc_start: 0.7391 (m-10) cc_final: 0.7132 (m-10) REVERT: F 225 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7272 (tppp) outliers start: 56 outliers final: 29 residues processed: 261 average time/residue: 0.6422 time to fit residues: 203.1784 Evaluate side-chains 254 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [294, 34, 138, 68, 94, 175, 298, 136, 272, 85, 345] chunk 294 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 345 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.064380 restraints weight = 163448.334| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.40 r_work: 0.2777 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34692 Z= 0.158 Angle : 0.705 15.968 47439 Z= 0.327 Chirality : 0.053 0.657 5595 Planarity : 0.004 0.062 6003 Dihedral : 4.929 69.914 4585 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 1.81 % Allowed : 8.26 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4233 helix: 1.83 (0.20), residues: 705 sheet: 0.42 (0.14), residues: 1344 loop : -0.96 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 44 TYR 0.022 0.001 TYR B 160 PHE 0.025 0.002 PHE B 133 TRP 0.018 0.001 TRP D 178 HIS 0.003 0.001 HIS H 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (34569) covalent geometry : angle 0.63165 / 0.31 (47121) SS BOND : bond 0.00360 / 0.21 ( 51) SS BOND : angle 1.55929 / 1.01 ( 102) hydrogen bonds : bond 0.04146 / 2.76 ( 1400) hydrogen bonds : angle 5.60304 / 3.91 ( 4056) link_BETA1-4 : bond 0.00258 / 0.15 ( 21) link_BETA1-4 : angle 2.07397 / 1.29 ( 63) link_NAG-ASN : bond 0.01520 / 0.81 ( 51) link_NAG-ASN : angle 5.28862 / 3.43 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 101 GLN cc_start: 0.7372 (tp-100) cc_final: 0.6634 (tp-100) REVERT: D 172 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8316 (mm-30) REVERT: C 603 ASN cc_start: 0.7322 (m110) cc_final: 0.6646 (p0) REVERT: C 619 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7050 (pt0) REVERT: L 142 PHE cc_start: 0.3568 (m-80) cc_final: 0.2705 (m-10) REVERT: L 219 GLU cc_start: 0.6734 (tp30) cc_final: 0.6317 (tp30) REVERT: H 146 PHE cc_start: 0.7416 (m-80) cc_final: 0.6996 (m-10) REVERT: B 130 VAL cc_start: 0.8301 (m) cc_final: 0.8017 (t) REVERT: B 314 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: F 101 GLN cc_start: 0.8107 (tt0) cc_final: 0.7755 (tt0) REVERT: F 225 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7208 (tppp) outliers start: 62 outliers final: 33 residues processed: 267 average time/residue: 0.6437 time to fit residues: 207.9288 Evaluate side-chains 261 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [94, 300, 264, 84, 408, 67, 13, 294, 70, 287, 59] chunk 94 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 408 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 287 optimal weight: 0.0670 chunk 59 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.065519 restraints weight = 146257.921| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.24 r_work: 0.2810 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34692 Z= 0.127 Angle : 0.673 15.061 47439 Z= 0.311 Chirality : 0.052 0.604 5595 Planarity : 0.004 0.060 6003 Dihedral : 4.770 69.089 4585 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 1.42 % Allowed : 8.95 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 4233 helix: 1.99 (0.20), residues: 705 sheet: 0.42 (0.14), residues: 1356 loop : -0.93 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 44 TYR 0.020 0.001 TYR B 160 PHE 0.025 0.001 PHE F 146 TRP 0.023 0.001 TRP D 178 HIS 0.003 0.000 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (34569) covalent geometry : angle 0.60509 / 0.30 (47121) SS BOND : bond 0.00269 / 0.17 ( 51) SS BOND : angle 1.18355 / 0.78 ( 102) hydrogen bonds : bond 0.03818 / 2.54 ( 1400) hydrogen bonds : angle 5.43532 / 3.79 ( 4056) link_BETA1-4 : bond 0.00292 / 0.17 ( 21) link_BETA1-4 : angle 2.01621 / 1.25 ( 63) link_NAG-ASN : bond 0.01492 / 0.81 ( 51) link_NAG-ASN : angle 4.99416 / 3.22 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6597 (tp30) cc_final: 0.6308 (tp30) REVERT: D 172 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8362 (mm-30) REVERT: C 134 GLN cc_start: 0.7692 (tp40) cc_final: 0.7426 (mm110) REVERT: L 103 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7233 (mm-30) REVERT: L 142 PHE cc_start: 0.3542 (m-80) cc_final: 0.2651 (m-10) REVERT: L 219 GLU cc_start: 0.6665 (tp30) cc_final: 0.6188 (tp30) REVERT: H 146 PHE cc_start: 0.7400 (m-80) cc_final: 0.6988 (m-10) REVERT: B 130 VAL cc_start: 0.8199 (m) cc_final: 0.7933 (t) REVERT: B 242 LEU cc_start: 0.8958 (mp) cc_final: 0.8747 (mp) REVERT: G 142 PHE cc_start: 0.3885 (m-10) cc_final: 0.3281 (m-10) REVERT: F 101 GLN cc_start: 0.8042 (tt0) cc_final: 0.7648 (tt0) REVERT: F 221 ASN cc_start: 0.5931 (m110) cc_final: 0.5670 (m110) REVERT: F 225 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7128 (tppp) outliers start: 48 outliers final: 29 residues processed: 267 average time/residue: 0.6391 time to fit residues: 207.7548 Evaluate side-chains 259 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [347, 102, 323, 319, 225, 118, 302, 384, 424, 423, 272] chunk 347 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 302 optimal weight: 4.9990 chunk 384 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 chunk 423 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN H 221 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.064868 restraints weight = 134040.525| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.10 r_work: 0.2798 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34692 Z= 0.160 Angle : 0.693 14.615 47439 Z= 0.321 Chirality : 0.053 0.726 5595 Planarity : 0.004 0.060 6003 Dihedral : 4.862 69.284 4585 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.59 % Rotamer: Outliers : 1.42 % Allowed : 9.87 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4233 helix: 1.95 (0.20), residues: 705 sheet: 0.37 (0.14), residues: 1320 loop : -0.91 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 44 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.001 PHE B 133 TRP 0.026 0.001 TRP D 178 HIS 0.004 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (34569) covalent geometry : angle 0.62538 / 0.31 (47121) SS BOND : bond 0.00284 / 0.18 ( 51) SS BOND : angle 1.19931 / 0.78 ( 102) hydrogen bonds : bond 0.04041 / 2.70 ( 1400) hydrogen bonds : angle 5.47578 / 3.82 ( 4056) link_BETA1-4 : bond 0.00272 / 0.16 ( 21) link_BETA1-4 : angle 2.03233 / 1.26 ( 63) link_NAG-ASN : bond 0.01429 / 0.77 ( 51) link_NAG-ASN : angle 5.07707 / 3.34 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6563 (tp30) cc_final: 0.6289 (tp30) REVERT: D 101 GLN cc_start: 0.7211 (tp-100) cc_final: 0.6471 (tp-100) REVERT: D 172 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8368 (mm-30) REVERT: C 134 GLN cc_start: 0.7760 (tp40) cc_final: 0.7501 (mm110) REVERT: L 219 GLU cc_start: 0.6644 (tp30) cc_final: 0.6086 (tp30) REVERT: H 146 PHE cc_start: 0.7412 (m-80) cc_final: 0.6964 (m-10) REVERT: B 130 VAL cc_start: 0.8504 (m) cc_final: 0.8194 (t) REVERT: B 314 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8456 (tm-30) REVERT: G 142 PHE cc_start: 0.3848 (m-10) cc_final: 0.3272 (m-10) REVERT: F 101 GLN cc_start: 0.8079 (tt0) cc_final: 0.7609 (tt0) REVERT: F 225 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7131 (tppp) outliers start: 48 outliers final: 37 residues processed: 259 average time/residue: 0.6204 time to fit residues: 194.9920 Evaluate side-chains 264 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [83, 326, 60, 165, 263, 221, 74, 252, 48, 38, 231] chunk 83 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 221 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.064572 restraints weight = 159582.453| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.37 r_work: 0.2783 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34692 Z= 0.151 Angle : 0.681 14.018 47439 Z= 0.317 Chirality : 0.052 0.579 5595 Planarity : 0.005 0.083 6003 Dihedral : 4.830 69.229 4585 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.56 % Rotamer: Outliers : 1.45 % Allowed : 10.20 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4233 helix: 1.97 (0.20), residues: 705 sheet: 0.36 (0.14), residues: 1320 loop : -0.91 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 44 TYR 0.019 0.001 TYR B1067 PHE 0.024 0.001 PHE F 146 TRP 0.030 0.001 TRP F 178 HIS 0.003 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (34569) covalent geometry : angle 0.61621 / 0.30 (47121) SS BOND : bond 0.00269 / 0.17 ( 51) SS BOND : angle 1.10674 / 0.73 ( 102) hydrogen bonds : bond 0.03988 / 2.66 ( 1400) hydrogen bonds : angle 5.45254 / 3.80 ( 4056) link_BETA1-4 : bond 0.00289 / 0.16 ( 21) link_BETA1-4 : angle 2.01951 / 1.25 ( 63) link_NAG-ASN : bond 0.01404 / 0.76 ( 51) link_NAG-ASN : angle 4.92365 / 3.23 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6683 (tp30) cc_final: 0.6392 (tp30) REVERT: D 101 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6547 (tp-100) REVERT: D 172 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8348 (mm-30) REVERT: C 134 GLN cc_start: 0.7746 (tp40) cc_final: 0.7491 (mm110) REVERT: C 1129 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8875 (m) REVERT: L 69 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8241 (pttp) REVERT: L 142 PHE cc_start: 0.3234 (m-10) cc_final: 0.2878 (m-10) REVERT: L 219 GLU cc_start: 0.6639 (tp30) cc_final: 0.6138 (tp30) REVERT: H 146 PHE cc_start: 0.7420 (m-80) cc_final: 0.6927 (m-10) REVERT: B 314 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: B 808 ASP cc_start: 0.7385 (t0) cc_final: 0.7174 (t0) REVERT: G 142 PHE cc_start: 0.3869 (m-10) cc_final: 0.3299 (m-10) REVERT: G 231 LYS cc_start: 0.5279 (tptt) cc_final: 0.5054 (tptm) REVERT: F 101 GLN cc_start: 0.8076 (tt0) cc_final: 0.7636 (tt0) REVERT: F 225 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.7015 (tppp) outliers start: 49 outliers final: 38 residues processed: 258 average time/residue: 0.6456 time to fit residues: 202.4935 Evaluate side-chains 266 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [223, 177, 225, 345, 113, 398, 202, 109, 35, 199, 327] chunk 223 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 398 optimal weight: 0.5980 chunk 202 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 221 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.063998 restraints weight = 135826.096| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.10 r_work: 0.2773 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34692 Z= 0.199 Angle : 0.710 13.723 47439 Z= 0.335 Chirality : 0.053 0.587 5595 Planarity : 0.005 0.069 6003 Dihedral : 5.006 69.784 4585 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.28 % Rotamer: Outliers : 1.45 % Allowed : 10.34 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4233 helix: 1.80 (0.20), residues: 708 sheet: 0.30 (0.14), residues: 1323 loop : -0.95 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 44 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.002 PHE C 133 TRP 0.037 0.002 TRP F 178 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (34569) covalent geometry : angle 0.65021 / 0.32 (47121) SS BOND : bond 0.00287 / 0.19 ( 51) SS BOND : angle 1.28416 / 0.83 ( 102) hydrogen bonds : bond 0.04327 / 2.89 ( 1400) hydrogen bonds : angle 5.56924 / 3.89 ( 4056) link_BETA1-4 : bond 0.00268 / 0.15 ( 21) link_BETA1-4 : angle 2.03345 / 1.26 ( 63) link_NAG-ASN : bond 0.01354 / 0.72 ( 51) link_NAG-ASN : angle 4.82914 / 3.19 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 101 GLN cc_start: 0.7213 (tp-100) cc_final: 0.6701 (tp40) REVERT: D 146 PHE cc_start: 0.6372 (m-10) cc_final: 0.6167 (m-80) REVERT: C 134 GLN cc_start: 0.7733 (tp40) cc_final: 0.7414 (mm110) REVERT: C 1129 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8885 (m) REVERT: L 44 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7988 (ttm110) REVERT: L 219 GLU cc_start: 0.6663 (tp30) cc_final: 0.6158 (tp30) REVERT: H 146 PHE cc_start: 0.7425 (m-80) cc_final: 0.6919 (m-10) REVERT: B 314 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: G 142 PHE cc_start: 0.3870 (m-10) cc_final: 0.3289 (m-10) REVERT: F 101 GLN cc_start: 0.8106 (tt0) cc_final: 0.7653 (tt0) REVERT: F 225 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7059 (tppp) outliers start: 49 outliers final: 39 residues processed: 266 average time/residue: 0.6395 time to fit residues: 205.7582 Evaluate side-chains 272 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [367, 276, 281, 29, 179, 403, 171, 209, 399, 96, 402] chunk 367 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 281 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 179 optimal weight: 0.6980 chunk 403 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 209 optimal weight: 0.0570 chunk 399 optimal weight: 9.9990 chunk 96 optimal weight: 0.0770 chunk 402 optimal weight: 5.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.065488 restraints weight = 141278.747| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.19 r_work: 0.2805 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 34692 Z= 0.121 Angle : 0.688 15.842 47439 Z= 0.320 Chirality : 0.053 1.064 5595 Planarity : 0.005 0.062 6003 Dihedral : 4.837 69.542 4585 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 1.14 % Allowed : 10.81 % Favored : 88.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4233 helix: 1.99 (0.20), residues: 705 sheet: 0.33 (0.14), residues: 1323 loop : -0.90 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 44 TYR 0.018 0.001 TYR B1067 PHE 0.024 0.001 PHE F 146 TRP 0.044 0.002 TRP F 178 HIS 0.003 0.000 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34569) covalent geometry : angle 0.62431 / 0.31 (47121) SS BOND : bond 0.00219 / 0.15 ( 51) SS BOND : angle 1.09621 / 0.73 ( 102) hydrogen bonds : bond 0.03800 / 2.52 ( 1400) hydrogen bonds : angle 5.42689 / 3.78 ( 4056) link_BETA1-4 : bond 0.00319 / 0.17 ( 21) link_BETA1-4 : angle 2.00937 / 1.25 ( 63) link_NAG-ASN : bond 0.01459 / 0.82 ( 51) link_NAG-ASN : angle 4.93112 / 3.23 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 GLU cc_start: 0.6439 (tp30) cc_final: 0.6193 (tp30) REVERT: E 221 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.7134 (p) REVERT: D 101 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6586 (tp-100) REVERT: D 223 ASN cc_start: 0.7055 (t0) cc_final: 0.6854 (t0) REVERT: C 134 GLN cc_start: 0.7758 (tp40) cc_final: 0.7469 (mm110) REVERT: C 1129 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8899 (m) REVERT: L 44 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7915 (ttm110) REVERT: L 219 GLU cc_start: 0.6583 (tp30) cc_final: 0.6071 (tp30) REVERT: H 146 PHE cc_start: 0.7439 (m-80) cc_final: 0.6945 (m-10) REVERT: B 314 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8462 (tm-30) REVERT: G 142 PHE cc_start: 0.3821 (m-10) cc_final: 0.3233 (m-10) REVERT: F 101 GLN cc_start: 0.8043 (tt0) cc_final: 0.7556 (tt0) REVERT: F 225 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7085 (tppp) outliers start: 38 outliers final: 24 residues processed: 251 average time/residue: 0.6457 time to fit residues: 196.0036 Evaluate side-chains 253 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [104, 12, 359, 97, 113, 347, 85, 281, 144, 154, 345] chunk 104 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 359 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 347 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 281 optimal weight: 0.0870 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 345 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS C 580 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN B 580 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066360 restraints weight = 118558.821| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.87 r_work: 0.2841 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34692 Z= 0.122 Angle : 0.663 13.112 47439 Z= 0.310 Chirality : 0.051 0.535 5595 Planarity : 0.004 0.059 6003 Dihedral : 4.699 68.496 4585 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.25 % Favored : 96.54 % Rotamer: Outliers : 1.08 % Allowed : 10.87 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4233 helix: 2.03 (0.20), residues: 711 sheet: 0.38 (0.14), residues: 1317 loop : -0.82 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 44 TYR 0.023 0.001 TYR E 73 PHE 0.024 0.001 PHE F 146 TRP 0.042 0.002 TRP D 178 HIS 0.003 0.000 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (34569) covalent geometry : angle 0.60546 / 0.30 (47121) SS BOND : bond 0.00227 / 0.15 ( 51) SS BOND : angle 0.99521 / 0.67 ( 102) hydrogen bonds : bond 0.03710 / 2.47 ( 1400) hydrogen bonds : angle 5.29133 / 3.68 ( 4056) link_BETA1-4 : bond 0.00321 / 0.18 ( 21) link_BETA1-4 : angle 1.95751 / 1.21 ( 63) link_NAG-ASN : bond 0.01262 / 0.71 ( 51) link_NAG-ASN : angle 4.61221 / 3.03 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10924.74 seconds wall clock time: 186 minutes 48.10 seconds (11208.10 seconds total)