Starting phenix.real_space_refine on Mon Jul 6 07:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw5_24063/07_2026/7mw5_24063.map" } resolution = 3.42 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 149 5.16 5 C 21357 2.51 5 N 5503 2.21 5 O 6626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33635 Number of models: 1 Model: "" Number of chains: 41 Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1541 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8149 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8140 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8140 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8320 Chain: "B" Number of atoms: 8145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8315 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 202} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1541 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 8145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Conformer: "B" Number of residues, atoms: 1057, 8136 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 53, 'TRANS': 1003} Chain breaks: 6 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 bond proxies already assigned to first conformer: 8315 Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 843 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 3 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 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 Time building chain proxies: 10.65, per 1000 atoms: 0.32 Number of scatterers: 33635 At special positions: 0 Unit cell: (164.472, 163.404, 248.844, 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 149 16.00 O 6626 8.00 N 5503 7.00 C 21357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 245 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 245 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 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 331 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 234 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 234 " " NAG I 1 " - " ASN C 282 " " NAG J 1 " - " ASN C 125 " " NAG K 1 " - " ASN C 331 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN B 17 " " NAG c 1 " - " ASN A 61 " " NAG d 1 " - " ASN A 282 " " NAG e 1 " - " ASN A 125 " " NAG f 1 " - " ASN A1134 " " NAG g 1 " - " ASN A1098 " " NAG h 1 " - " ASN A 801 " " NAG i 1 " - " ASN A 717 " " NAG j 1 " - " ASN A 709 " " NAG k 1 " - " ASN A 343 " " NAG l 1 " - " ASN A 17 " NAG-THR " NAG B1306 " - " THR B 124 " Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 2.3 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7912 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 77 sheets defined 18.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 172 through 178 Processing helix chain 'L' and resid 234 through 239 Processing helix chain 'H' and resid 81 through 84 Processing helix chain 'H' and resid 237 through 242 removed outlier: 3.834A pdb=" N THR H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.927A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.511A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.784A pdb=" N LEU C 441 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 442 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.364A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 6.011A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.579A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.875A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.191A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.596A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.663A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.309A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.715A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 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: 4.093A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 921 through 941 removed outlier: 5.878A pdb=" N PHE B 927 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.755A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.537A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 172 through 179 removed outlier: 3.648A pdb=" N SER G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY G 179 " --> pdb=" O GLN G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 4.107A pdb=" N HIS G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.908A pdb=" N GLY F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR F 241 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.822A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.090A 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 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.791A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.661A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.930A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.062A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.610A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.353A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 1032 removed outlier: 3.600A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.548A pdb=" N THR E 54 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.570A pdb=" N PHE L 95 " --> pdb=" O CYS L 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'L' and resid 69 through 72 removed outlier: 6.509A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 69 through 72 removed outlier: 6.509A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 165 through 169 Processing sheet with id=AA6, first strand: chain 'L' and resid 205 through 206 removed outlier: 4.785A pdb=" N TRP L 199 " --> pdb=" O GLN L 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.566A pdb=" N CYS H 41 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA H 98 " --> pdb=" O CYS H 41 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.676A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.694A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 170 through 174 removed outlier: 5.694A pdb=" N TYR H 226 " --> pdb=" O ASP H 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 201 through 204 removed outlier: 4.512A pdb=" N TYR H 244 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.915A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.847A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.158A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.836A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.080A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.466A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 325 through 326 removed outlier: 4.895A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.990A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.857A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.814A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 721 through 728 removed outlier: 7.078A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 721 through 728 Processing sheet with id=AC8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 removed outlier: 3.561A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AD2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.917A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.070A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.601A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.114A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 196 through 197 Processing sheet with id=AD8, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.599A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.741A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.569A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.388A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'B' and resid 721 through 728 removed outlier: 6.851A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.415A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.619A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1080 through 1082 Processing sheet with id=AE9, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AF1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AF3, first strand: chain 'G' and resid 30 through 33 Processing sheet with id=AF4, first strand: chain 'G' and resid 69 through 70 Processing sheet with id=AF5, first strand: chain 'G' and resid 165 through 169 removed outlier: 3.847A pdb=" N SER G 165 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER G 182 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU G 232 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL G 184 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU G 230 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU G 186 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER G 228 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN G 188 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU G 226 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER G 225 " --> pdb=" O THR G 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 195 through 201 Processing sheet with id=AF7, first strand: chain 'F' and resid 24 through 26 removed outlier: 3.672A pdb=" N CYS F 41 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 98 " --> pdb=" O CYS F 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR F 99 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR F 90 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 101 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS F 86 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 77 through 79 removed outlier: 5.935A pdb=" N TRP F 66 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS F 57 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE F 70 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET F 53 " --> pdb=" O ILE F 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.879A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.879A pdb=" N TYR F 226 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 201 through 204 Processing sheet with id=AG3, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.754A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.649A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.270A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AG7, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.746A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.278A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.009A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.571A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AH3, first strand: chain 'A' and resid 721 through 728 removed outlier: 6.827A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 721 through 728 Processing sheet with id=AH5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AH6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AH7, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AH8, first strand: chain 'A' and resid 1093 through 1097 Processing sheet with id=AH9, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AI1, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.574A pdb=" N GLU E 129 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.500A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 24 through 26 Processing sheet with id=AI4, first strand: chain 'D' and resid 77 through 79 removed outlier: 5.903A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 70 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 53 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR D 127 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 87 through 92 1176 hydrogen bonds defined for protein. 3159 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: 8.64 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10570 1.34 - 1.46: 7950 1.46 - 1.58: 15670 1.58 - 1.70: 0 1.70 - 1.82: 194 Bond restraints: 34384 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 34379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 45702 2.11 - 4.22: 1006 4.22 - 6.33: 95 6.33 - 8.44: 19 8.44 - 10.55: 2 Bond angle restraints: 46824 Sorted by residual: angle pdb=" C ALA B1070 " pdb=" N GLN B1071 " pdb=" CA GLN B1071 " ideal model delta sigma weight residual 121.33 128.42 -7.09 1.40e+00 5.10e-01 2.57e+01 angle pdb=" C LEU C 212 " pdb=" CA LEU C 212 " pdb=" CB LEU C 212 " ideal model delta sigma weight residual 115.79 110.12 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" CA CYS H 115 " pdb=" CB CYS H 115 " pdb=" SG CYS H 115 " ideal model delta sigma weight residual 114.40 124.95 -10.55 2.30e+00 1.89e-01 2.11e+01 angle pdb=" N ALA B1070 " pdb=" CA ALA B1070 " pdb=" C ALA B1070 " ideal model delta sigma weight residual 107.32 114.80 -7.48 1.65e+00 3.67e-01 2.06e+01 angle pdb=" C LYS B1086 " pdb=" N ALA B1087 " pdb=" CA ALA B1087 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.70e+01 ... (remaining 46819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 18019 17.64 - 35.27: 1459 35.27 - 52.91: 234 52.91 - 70.54: 63 70.54 - 88.18: 27 Dihedral angle restraints: 19802 sinusoidal: 7489 harmonic: 12313 Sorted by residual: 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 -113.36 -66.64 0 5.00e+00 4.00e-02 1.78e+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 -114.49 -65.51 0 5.00e+00 4.00e-02 1.72e+02 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 -116.42 -63.58 0 5.00e+00 4.00e-02 1.62e+02 ... (remaining 19799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 5559 0.255 - 0.510: 10 0.510 - 0.764: 3 0.764 - 1.019: 0 1.019 - 1.274: 1 Chirality restraints: 5573 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 5570 not shown) Planarity restraints: 5979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " 0.032 2.00e-02 2.50e+03 2.93e-02 1.07e+01 pdb=" CG ASN A 17 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 100 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO L 101 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO L 101 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 101 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 27 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C SER G 27 " -0.055 2.00e-02 2.50e+03 pdb=" O SER G 27 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO G 28 " 0.019 2.00e-02 2.50e+03 ... (remaining 5976 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 993 2.69 - 3.24: 33937 3.24 - 3.80: 53864 3.80 - 4.35: 71608 4.35 - 4.90: 115515 Nonbonded interactions: 275917 Sorted by model distance: nonbonded pdb=" OD2 ASP C 796 " pdb=" O6 NAG Z 1 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR G 60 " pdb=" O ARG F 119 " model vdw 2.166 3.040 nonbonded pdb=" NE2 GLN D 25 " pdb=" O TYR D 113 " model vdw 2.168 3.120 nonbonded pdb=" ND2 ASN F 54 " pdb=" O SER F 118 " model vdw 2.169 3.120 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.178 3.040 ... (remaining 275912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1308)) selection = (chain 'B' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1308)) selection = (chain 'C' and (resid 15 through 145 or resid 152 through 1009 or resid 1011 thr \ ough 1308)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 36.250 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 34512 Z= 0.204 Angle : 0.796 23.169 47159 Z= 0.400 Chirality : 0.053 1.274 5573 Planarity : 0.005 0.082 5929 Dihedral : 13.493 88.180 11746 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.96 % Favored : 91.47 % Rotamer: Outliers : 0.11 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.13), residues: 4193 helix: 0.78 (0.20), residues: 670 sheet: -0.95 (0.16), residues: 1064 loop : -1.99 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 85 TYR 0.020 0.001 TYR C 505 PHE 0.027 0.002 PHE C 906 TRP 0.033 0.002 TRP F 55 HIS 0.004 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (34384) covalent geometry : angle 0.72879 / 0.39 (46824) SS BOND : bond 0.00237 / 0.15 ( 48) SS BOND : angle 1.42570 / 1.00 ( 96) hydrogen bonds : bond 0.17328 / 11.55 ( 1117) hydrogen bonds : angle 7.68385 / 5.23 ( 3159) link_BETA1-4 : bond 0.00475 / 0.33 ( 29) link_BETA1-4 : angle 2.65542 / 1.94 ( 87) link_NAG-ASN : bond 0.00858 / 0.61 ( 50) link_NAG-ASN : angle 5.27026 / 3.45 ( 150) link_NAG-THR : bond 0.00180 / 0.09 ( 1) link_NAG-THR : angle 0.94033 / 0.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 53 MET cc_start: 0.8574 (mtt) cc_final: 0.8272 (mtt) REVERT: C 248 TYR cc_start: 0.4625 (m-10) cc_final: 0.4235 (m-10) REVERT: F 84 LYS cc_start: 0.7060 (mmtt) cc_final: 0.6568 (mmmt) REVERT: F 100 MET cc_start: 0.7461 (mmp) cc_final: 0.7159 (mmt) REVERT: F 204 TRP cc_start: 0.5671 (m100) cc_final: 0.5379 (m100) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.1936 time to fit residues: 73.9274 Evaluate side-chains 159 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0040 chunk 401 optimal weight: 0.3980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 HIS ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 GLN H 25 GLN H 125 GLN H 214 HIS ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN C 69 HIS C 388 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN B 641 ASN B 901 GLN G 211 GLN F 125 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 901 GLN E 26 GLN E 100 HIS E 113 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.081470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060842 restraints weight = 273639.440| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.78 r_work: 0.3099 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34512 Z= 0.144 Angle : 0.730 21.407 47159 Z= 0.358 Chirality : 0.052 0.840 5573 Planarity : 0.005 0.069 5929 Dihedral : 5.678 65.929 4521 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.13 % Favored : 91.35 % Rotamer: Outliers : 0.56 % Allowed : 4.60 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.13), residues: 4193 helix: 1.19 (0.20), residues: 670 sheet: -0.83 (0.16), residues: 1042 loop : -1.94 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 117 TYR 0.026 0.002 TYR B 265 PHE 0.025 0.002 PHE F 48 TRP 0.029 0.002 TRP G 59 HIS 0.011 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (34384) covalent geometry : angle 0.67595 / 0.35 (46824) SS BOND : bond 0.00259 / 0.16 ( 48) SS BOND : angle 1.35483 / 0.95 ( 96) hydrogen bonds : bond 0.04525 / 3.01 ( 1117) hydrogen bonds : angle 6.28872 / 4.26 ( 3159) link_BETA1-4 : bond 0.00563 / 0.42 ( 29) link_BETA1-4 : angle 1.91805 / 1.35 ( 87) link_NAG-ASN : bond 0.00775 / 0.54 ( 50) link_NAG-ASN : angle 4.64258 / 3.05 ( 150) link_NAG-THR : bond 0.00226 / 0.12 ( 1) link_NAG-THR : angle 0.35817 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 44 ARG cc_start: 0.8714 (tmt-80) cc_final: 0.8461 (tpt170) REVERT: L 57 MET cc_start: 0.6450 (ttm) cc_final: 0.6235 (ttm) REVERT: L 73 TYR cc_start: 0.8033 (m-80) cc_final: 0.7536 (m-80) REVERT: H 65 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6486 (tm-30) REVERT: H 172 PHE cc_start: 0.6974 (m-10) cc_final: 0.6720 (m-80) REVERT: B 118 LEU cc_start: 0.8448 (tt) cc_final: 0.8181 (pp) REVERT: B 338 PHE cc_start: 0.6871 (p90) cc_final: 0.6663 (p90) REVERT: F 109 ASP cc_start: 0.7529 (t0) cc_final: 0.7117 (t0) REVERT: F 119 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7789 (mtm-85) REVERT: F 122 TYR cc_start: 0.6686 (t80) cc_final: 0.6335 (t80) REVERT: F 204 TRP cc_start: 0.5611 (m100) cc_final: 0.5225 (m100) REVERT: A 177 MET cc_start: 0.4719 (ppp) cc_final: 0.4152 (ppp) REVERT: E 40 THR cc_start: 0.6273 (m) cc_final: 0.5925 (m) REVERT: E 107 ILE cc_start: 0.6111 (mm) cc_final: 0.5907 (mm) REVERT: D 82 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5573 (ptpt) outliers start: 18 outliers final: 9 residues processed: 194 average time/residue: 0.2137 time to fit residues: 70.7337 Evaluate side-chains 165 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 82 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 379 optimal weight: 1.9990 chunk 351 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 229 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 393 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 955 ASN F 58 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** E 114 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 = 0.3909 r_free = 0.3909 target = 0.081030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058966 restraints weight = 267523.918| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.45 r_work: 0.3107 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34512 Z= 0.210 Angle : 0.746 21.209 47159 Z= 0.365 Chirality : 0.052 0.804 5573 Planarity : 0.005 0.071 5929 Dihedral : 5.727 65.347 4521 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.65 % Favored : 90.87 % Rotamer: Outliers : 0.84 % Allowed : 6.82 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.13), residues: 4193 helix: 1.18 (0.20), residues: 670 sheet: -0.84 (0.16), residues: 1050 loop : -1.97 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 117 TYR 0.026 0.002 TYR A 473 PHE 0.030 0.002 PHE C 906 TRP 0.029 0.002 TRP G 59 HIS 0.027 0.002 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (34384) covalent geometry : angle 0.69425 / 0.35 (46824) SS BOND : bond 0.00430 / 0.21 ( 48) SS BOND : angle 1.52040 / 1.01 ( 96) hydrogen bonds : bond 0.04473 / 2.99 ( 1117) hydrogen bonds : angle 6.08010 / 4.12 ( 3159) link_BETA1-4 : bond 0.00404 / 0.30 ( 29) link_BETA1-4 : angle 1.85880 / 1.30 ( 87) link_NAG-ASN : bond 0.00706 / 0.50 ( 50) link_NAG-ASN : angle 4.59698 / 3.01 ( 150) link_NAG-THR : bond 0.00131 / 0.07 ( 1) link_NAG-THR : angle 0.36675 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 57 MET cc_start: 0.6404 (ttm) cc_final: 0.6183 (ttm) REVERT: L 73 TYR cc_start: 0.8045 (m-80) cc_final: 0.7619 (m-80) REVERT: H 65 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6881 (tm-30) REVERT: H 100 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8127 (tpt) REVERT: H 172 PHE cc_start: 0.6886 (m-10) cc_final: 0.6645 (m-80) REVERT: B 338 PHE cc_start: 0.6797 (p90) cc_final: 0.6573 (p90) REVERT: F 109 ASP cc_start: 0.7443 (t0) cc_final: 0.6219 (p0) REVERT: F 113 TYR cc_start: 0.7970 (m-10) cc_final: 0.7648 (m-10) REVERT: F 204 TRP cc_start: 0.5899 (m100) cc_final: 0.5590 (m100) REVERT: A 68 ILE cc_start: 0.6607 (mm) cc_final: 0.6144 (mt) REVERT: A 177 MET cc_start: 0.4592 (ppp) cc_final: 0.4044 (ppp) REVERT: E 40 THR cc_start: 0.6248 (m) cc_final: 0.5959 (m) REVERT: E 107 ILE cc_start: 0.6131 (mm) cc_final: 0.5852 (mm) REVERT: D 82 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5601 (ptpt) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 0.1925 time to fit residues: 62.1371 Evaluate side-chains 174 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 82 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 234 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 380 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 357 optimal weight: 0.8980 chunk 328 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN G 211 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.080790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.059339 restraints weight = 231683.658| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.99 r_work: 0.3137 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34512 Z= 0.159 Angle : 0.709 20.595 47159 Z= 0.345 Chirality : 0.051 0.739 5573 Planarity : 0.005 0.073 5929 Dihedral : 5.627 65.103 4521 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.41 % Favored : 91.23 % Rotamer: Outliers : 0.87 % Allowed : 8.64 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.13), residues: 4193 helix: 1.25 (0.20), residues: 674 sheet: -0.87 (0.16), residues: 1055 loop : -1.93 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.028 0.001 TYR A 473 PHE 0.028 0.002 PHE L 169 TRP 0.026 0.002 TRP G 59 HIS 0.019 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (34384) covalent geometry : angle 0.65881 / 0.33 (46824) SS BOND : bond 0.00290 / 0.16 ( 48) SS BOND : angle 1.14104 / 0.82 ( 96) hydrogen bonds : bond 0.04027 / 2.67 ( 1117) hydrogen bonds : angle 5.87181 / 3.98 ( 3159) link_BETA1-4 : bond 0.00418 / 0.31 ( 29) link_BETA1-4 : angle 1.78459 / 1.26 ( 87) link_NAG-ASN : bond 0.00716 / 0.51 ( 50) link_NAG-ASN : angle 4.45973 / 2.93 ( 150) link_NAG-THR : bond 0.00002 / 0.00 ( 1) link_NAG-THR : angle 0.43481 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 TYR cc_start: 0.7911 (m-80) cc_final: 0.7678 (m-80) REVERT: H 39 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8548 (mm) REVERT: H 65 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6834 (tm-30) REVERT: H 100 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8215 (tpt) REVERT: C 439 ASN cc_start: 0.8696 (m110) cc_final: 0.8469 (m110) REVERT: G 111 PHE cc_start: 0.5460 (m-80) cc_final: 0.5260 (m-80) REVERT: F 109 ASP cc_start: 0.7538 (t0) cc_final: 0.6272 (p0) REVERT: F 204 TRP cc_start: 0.5994 (m100) cc_final: 0.5714 (m100) REVERT: A 68 ILE cc_start: 0.6625 (mm) cc_final: 0.6161 (mt) REVERT: E 40 THR cc_start: 0.6175 (m) cc_final: 0.5902 (m) REVERT: E 106 ASP cc_start: 0.7547 (t0) cc_final: 0.7217 (t70) REVERT: E 107 ILE cc_start: 0.5943 (mm) cc_final: 0.5628 (mm) REVERT: D 82 LYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5592 (ptpt) outliers start: 29 outliers final: 19 residues processed: 193 average time/residue: 0.2021 time to fit residues: 67.2350 Evaluate side-chains 177 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 169 PHE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 214 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 82 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 393 optimal weight: 1.9990 chunk 269 optimal weight: 30.0000 chunk 228 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 380 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 506 GLN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.080480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059716 restraints weight = 304581.369| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 5.28 r_work: 0.3097 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34512 Z= 0.155 Angle : 0.702 20.291 47159 Z= 0.340 Chirality : 0.051 0.685 5573 Planarity : 0.005 0.073 5929 Dihedral : 5.546 64.109 4521 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.48 % Favored : 91.16 % Rotamer: Outliers : 0.95 % Allowed : 10.30 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.73 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 4193 helix: 1.35 (0.20), residues: 668 sheet: -0.85 (0.16), residues: 1041 loop : -1.88 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.024 0.001 TYR E 73 PHE 0.032 0.002 PHE D 48 TRP 0.026 0.002 TRP D 55 HIS 0.021 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (34384) covalent geometry : angle 0.65281 / 0.33 (46824) SS BOND : bond 0.00282 / 0.16 ( 48) SS BOND : angle 1.09134 / 0.78 ( 96) hydrogen bonds : bond 0.03899 / 2.59 ( 1117) hydrogen bonds : angle 5.76329 / 3.91 ( 3159) link_BETA1-4 : bond 0.00418 / 0.31 ( 29) link_BETA1-4 : angle 1.75617 / 1.23 ( 87) link_NAG-ASN : bond 0.00705 / 0.50 ( 50) link_NAG-ASN : angle 4.38842 / 2.88 ( 150) link_NAG-THR : bond 0.00045 / 0.02 ( 1) link_NAG-THR : angle 0.23793 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 TYR cc_start: 0.7978 (m-80) cc_final: 0.7760 (m-80) REVERT: H 39 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8514 (mm) REVERT: H 100 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8134 (tpt) REVERT: C 439 ASN cc_start: 0.8694 (m-40) cc_final: 0.8448 (m110) REVERT: F 109 ASP cc_start: 0.7471 (t0) cc_final: 0.7091 (t0) REVERT: F 113 TYR cc_start: 0.7948 (m-10) cc_final: 0.7706 (m-10) REVERT: F 204 TRP cc_start: 0.6079 (m100) cc_final: 0.5778 (m100) REVERT: A 68 ILE cc_start: 0.6675 (mm) cc_final: 0.6213 (mt) REVERT: E 40 THR cc_start: 0.6261 (m) cc_final: 0.6006 (m) REVERT: E 106 ASP cc_start: 0.7522 (t0) cc_final: 0.7146 (t70) REVERT: E 107 ILE cc_start: 0.6036 (mm) cc_final: 0.5692 (mm) REVERT: D 100 MET cc_start: 0.6997 (tmm) cc_final: 0.6267 (tmm) outliers start: 32 outliers final: 23 residues processed: 194 average time/residue: 0.2045 time to fit residues: 68.0755 Evaluate side-chains 176 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 169 PHE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 109 optimal weight: 1.9990 chunk 369 optimal weight: 0.8980 chunk 308 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 416 optimal weight: 20.0000 chunk 189 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 358 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.081299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.058974 restraints weight = 201475.404| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.82 r_work: 0.3111 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34512 Z= 0.142 Angle : 0.688 19.944 47159 Z= 0.333 Chirality : 0.050 0.612 5573 Planarity : 0.005 0.074 5929 Dihedral : 5.447 63.104 4521 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.37 % Favored : 91.32 % Rotamer: Outliers : 1.09 % Allowed : 10.86 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4193 helix: 1.43 (0.20), residues: 666 sheet: -0.85 (0.16), residues: 1044 loop : -1.83 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.023 0.001 TYR E 73 PHE 0.033 0.002 PHE L 169 TRP 0.031 0.002 TRP D 55 HIS 0.005 0.001 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (34384) covalent geometry : angle 0.63979 / 0.32 (46824) SS BOND : bond 0.00268 / 0.16 ( 48) SS BOND : angle 1.02514 / 0.74 ( 96) hydrogen bonds : bond 0.03742 / 2.47 ( 1117) hydrogen bonds : angle 5.63333 / 3.83 ( 3159) link_BETA1-4 : bond 0.00432 / 0.31 ( 29) link_BETA1-4 : angle 1.72058 / 1.20 ( 87) link_NAG-ASN : bond 0.00706 / 0.50 ( 50) link_NAG-ASN : angle 4.30076 / 2.82 ( 150) link_NAG-THR : bond 0.00035 / 0.02 ( 1) link_NAG-THR : angle 0.33487 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 44 ARG cc_start: 0.8780 (tmt-80) cc_final: 0.8558 (tpt170) REVERT: L 57 MET cc_start: 0.6384 (ttm) cc_final: 0.6154 (ttm) REVERT: L 73 TYR cc_start: 0.7754 (m-80) cc_final: 0.7522 (m-80) REVERT: H 39 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8614 (mm) REVERT: H 100 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8218 (tpt) REVERT: C 439 ASN cc_start: 0.8733 (m-40) cc_final: 0.8475 (m110) REVERT: F 109 ASP cc_start: 0.7554 (t0) cc_final: 0.7168 (t0) REVERT: F 113 TYR cc_start: 0.8033 (m-10) cc_final: 0.7806 (m-10) REVERT: F 204 TRP cc_start: 0.5991 (m100) cc_final: 0.5558 (m100) REVERT: A 68 ILE cc_start: 0.6845 (mm) cc_final: 0.6410 (mt) REVERT: E 40 THR cc_start: 0.6328 (m) cc_final: 0.6108 (m) REVERT: E 106 ASP cc_start: 0.7569 (t0) cc_final: 0.7146 (t70) REVERT: E 107 ILE cc_start: 0.6037 (mm) cc_final: 0.5669 (mm) REVERT: D 100 MET cc_start: 0.6992 (tmm) cc_final: 0.6567 (tmm) outliers start: 37 outliers final: 23 residues processed: 200 average time/residue: 0.2056 time to fit residues: 70.2554 Evaluate side-chains 180 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 169 PHE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 44 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 383 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 404 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN B 901 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 919 ASN E 113 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.079869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058132 restraints weight = 247127.431| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.28 r_work: 0.3055 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 34512 Z= 0.328 Angle : 0.848 19.717 47159 Z= 0.414 Chirality : 0.056 0.726 5573 Planarity : 0.006 0.074 5929 Dihedral : 6.012 62.748 4521 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.42 % Favored : 89.15 % Rotamer: Outliers : 1.32 % Allowed : 11.45 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.13), residues: 4193 helix: 0.84 (0.20), residues: 669 sheet: -1.06 (0.16), residues: 1010 loop : -2.01 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 117 TYR 0.035 0.002 TYR A 473 PHE 0.026 0.003 PHE D 48 TRP 0.024 0.002 TRP L 199 HIS 0.007 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.33 (34384) covalent geometry : angle 0.80218 / 0.40 (46824) SS BOND : bond 0.00412 / 0.24 ( 48) SS BOND : angle 1.50265 / 1.03 ( 96) hydrogen bonds : bond 0.04731 / 3.15 ( 1117) hydrogen bonds : angle 6.03716 / 4.11 ( 3159) link_BETA1-4 : bond 0.00466 / 0.35 ( 29) link_BETA1-4 : angle 1.97604 / 1.36 ( 87) link_NAG-ASN : bond 0.00708 / 0.50 ( 50) link_NAG-ASN : angle 4.63438 / 3.06 ( 150) link_NAG-THR : bond 0.00024 / 0.01 ( 1) link_NAG-THR : angle 0.53728 / 0.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 44 ARG cc_start: 0.8815 (tmt-80) cc_final: 0.8598 (tpt170) REVERT: H 100 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8293 (ptm) REVERT: C 439 ASN cc_start: 0.8809 (m-40) cc_final: 0.8562 (m110) REVERT: F 109 ASP cc_start: 0.7466 (t0) cc_final: 0.7253 (t0) REVERT: A 68 ILE cc_start: 0.6851 (mm) cc_final: 0.6397 (mt) REVERT: E 106 ASP cc_start: 0.7717 (t0) cc_final: 0.7323 (t70) REVERT: E 107 ILE cc_start: 0.6032 (mm) cc_final: 0.5639 (mm) REVERT: E 127 LYS cc_start: 0.7328 (pptt) cc_final: 0.6774 (pptt) outliers start: 45 outliers final: 35 residues processed: 189 average time/residue: 0.1924 time to fit residues: 63.9159 Evaluate side-chains 182 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 128 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 408 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 372 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 300 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 351 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN F 125 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** E 114 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 = 0.3918 r_free = 0.3918 target = 0.083065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060411 restraints weight = 273599.216| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.83 r_work: 0.3116 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.138 Angle : 0.705 19.703 47159 Z= 0.342 Chirality : 0.050 0.605 5573 Planarity : 0.005 0.071 5929 Dihedral : 5.577 62.336 4521 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.86 % Favored : 91.80 % Rotamer: Outliers : 0.73 % Allowed : 12.51 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 4193 helix: 1.28 (0.20), residues: 665 sheet: -0.87 (0.16), residues: 1015 loop : -1.88 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.023 0.001 TYR E 73 PHE 0.028 0.002 PHE L 167 TRP 0.028 0.002 TRP G 59 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (34384) covalent geometry : angle 0.65842 / 0.33 (46824) SS BOND : bond 0.00256 / 0.16 ( 48) SS BOND : angle 1.00719 / 0.73 ( 96) hydrogen bonds : bond 0.03725 / 2.45 ( 1117) hydrogen bonds : angle 5.66983 / 3.85 ( 3159) link_BETA1-4 : bond 0.00469 / 0.34 ( 29) link_BETA1-4 : angle 1.69799 / 1.20 ( 87) link_NAG-ASN : bond 0.00740 / 0.52 ( 50) link_NAG-ASN : angle 4.29546 / 2.83 ( 150) link_NAG-THR : bond 0.00142 / 0.07 ( 1) link_NAG-THR : angle 0.31623 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 439 ASN cc_start: 0.8741 (m-40) cc_final: 0.8471 (m110) REVERT: F 94 SER cc_start: 0.7775 (p) cc_final: 0.7538 (t) REVERT: F 109 ASP cc_start: 0.7395 (t0) cc_final: 0.7064 (t0) REVERT: F 113 TYR cc_start: 0.7902 (m-10) cc_final: 0.7618 (m-80) REVERT: A 68 ILE cc_start: 0.6979 (mm) cc_final: 0.6556 (mt) REVERT: E 40 THR cc_start: 0.6676 (m) cc_final: 0.6448 (m) REVERT: E 107 ILE cc_start: 0.6152 (mm) cc_final: 0.5783 (mm) REVERT: E 109 MET cc_start: 0.8446 (tpt) cc_final: 0.7998 (mmm) REVERT: E 127 LYS cc_start: 0.7165 (pptt) cc_final: 0.6464 (pptt) REVERT: D 100 MET cc_start: 0.6414 (tmm) cc_final: 0.5637 (tmm) outliers start: 24 outliers final: 22 residues processed: 190 average time/residue: 0.1985 time to fit residues: 65.6198 Evaluate side-chains 179 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 145 optimal weight: 2.9990 chunk 402 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 404 optimal weight: 0.0050 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.082412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059660 restraints weight = 218602.565| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.07 r_work: 0.3118 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34512 Z= 0.181 Angle : 0.720 19.340 47159 Z= 0.348 Chirality : 0.051 0.605 5573 Planarity : 0.005 0.072 5929 Dihedral : 5.567 61.658 4521 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.18 % Favored : 90.49 % Rotamer: Outliers : 0.95 % Allowed : 12.65 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.13), residues: 4193 helix: 1.29 (0.20), residues: 668 sheet: -0.92 (0.16), residues: 1019 loop : -1.88 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 44 TYR 0.024 0.002 TYR A 473 PHE 0.026 0.002 PHE F 48 TRP 0.042 0.002 TRP D 55 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (34384) covalent geometry : angle 0.67409 / 0.34 (46824) SS BOND : bond 0.00288 / 0.17 ( 48) SS BOND : angle 1.07873 / 0.77 ( 96) hydrogen bonds : bond 0.03898 / 2.58 ( 1117) hydrogen bonds : angle 5.65688 / 3.84 ( 3159) link_BETA1-4 : bond 0.00400 / 0.30 ( 29) link_BETA1-4 : angle 1.72902 / 1.21 ( 87) link_NAG-ASN : bond 0.00677 / 0.49 ( 50) link_NAG-ASN : angle 4.29531 / 2.83 ( 150) link_NAG-THR : bond 0.00147 / 0.08 ( 1) link_NAG-THR : angle 0.02452 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 44 ARG cc_start: 0.8979 (tpt170) cc_final: 0.8549 (tpt170) REVERT: L 73 TYR cc_start: 0.7963 (m-80) cc_final: 0.7608 (m-80) REVERT: H 100 MET cc_start: 0.8441 (mtm) cc_final: 0.7902 (mtm) REVERT: C 439 ASN cc_start: 0.8788 (m-40) cc_final: 0.8509 (m110) REVERT: F 94 SER cc_start: 0.7768 (p) cc_final: 0.7539 (t) REVERT: F 109 ASP cc_start: 0.7410 (t0) cc_final: 0.7029 (t0) REVERT: F 113 TYR cc_start: 0.8055 (m-10) cc_final: 0.7819 (m-10) REVERT: A 68 ILE cc_start: 0.6896 (mm) cc_final: 0.6485 (mt) REVERT: E 40 THR cc_start: 0.6705 (m) cc_final: 0.6464 (m) REVERT: E 107 ILE cc_start: 0.6259 (mm) cc_final: 0.5893 (mm) REVERT: E 127 LYS cc_start: 0.7264 (pptt) cc_final: 0.6676 (pptt) REVERT: D 100 MET cc_start: 0.6556 (tmm) cc_final: 0.5874 (tmm) outliers start: 32 outliers final: 27 residues processed: 185 average time/residue: 0.1998 time to fit residues: 63.5526 Evaluate side-chains 177 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 172 optimal weight: 0.0980 chunk 46 optimal weight: 0.0030 chunk 104 optimal weight: 2.9990 chunk 339 optimal weight: 0.0030 chunk 87 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 418 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 overall best weight: 0.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.080207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.058776 restraints weight = 265883.885| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 4.47 r_work: 0.3126 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.130 Angle : 0.693 19.201 47159 Z= 0.334 Chirality : 0.050 0.580 5573 Planarity : 0.005 0.072 5929 Dihedral : 5.429 61.114 4521 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.20 % Favored : 91.47 % Rotamer: Outliers : 0.90 % Allowed : 12.77 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.13), residues: 4193 helix: 1.47 (0.20), residues: 664 sheet: -0.83 (0.16), residues: 1018 loop : -1.83 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 454 TYR 0.019 0.001 TYR C 369 PHE 0.026 0.001 PHE F 48 TRP 0.042 0.002 TRP D 55 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (34384) covalent geometry : angle 0.64828 / 0.32 (46824) SS BOND : bond 0.00232 / 0.14 ( 48) SS BOND : angle 0.95197 / 0.69 ( 96) hydrogen bonds : bond 0.03636 / 2.40 ( 1117) hydrogen bonds : angle 5.50315 / 3.74 ( 3159) link_BETA1-4 : bond 0.00448 / 0.33 ( 29) link_BETA1-4 : angle 1.69436 / 1.19 ( 87) link_NAG-ASN : bond 0.00719 / 0.51 ( 50) link_NAG-ASN : angle 4.17254 / 2.75 ( 150) link_NAG-THR : bond 0.00210 / 0.11 ( 1) link_NAG-THR : angle 0.05785 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 TYR cc_start: 0.7972 (m-80) cc_final: 0.7605 (m-80) REVERT: G 190 PHE cc_start: 0.8722 (p90) cc_final: 0.8415 (p90) REVERT: F 94 SER cc_start: 0.7847 (p) cc_final: 0.7589 (t) REVERT: F 100 MET cc_start: 0.6402 (mmm) cc_final: 0.6133 (mmm) REVERT: F 109 ASP cc_start: 0.7412 (t0) cc_final: 0.7021 (t0) REVERT: F 113 TYR cc_start: 0.7883 (m-10) cc_final: 0.7680 (m-10) REVERT: A 68 ILE cc_start: 0.6969 (mm) cc_final: 0.6561 (mt) REVERT: E 40 THR cc_start: 0.6640 (m) cc_final: 0.6423 (m) REVERT: E 66 GLN cc_start: 0.7307 (mp10) cc_final: 0.7037 (pm20) REVERT: E 107 ILE cc_start: 0.6247 (mm) cc_final: 0.5930 (mm) REVERT: E 109 MET cc_start: 0.8491 (tpt) cc_final: 0.8000 (mmm) REVERT: E 127 LYS cc_start: 0.7332 (pptt) cc_final: 0.6549 (pptt) REVERT: D 100 MET cc_start: 0.6493 (tmm) cc_final: 0.5828 (tmm) outliers start: 30 outliers final: 28 residues processed: 181 average time/residue: 0.2013 time to fit residues: 62.8145 Evaluate side-chains 178 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 119 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 218 optimal weight: 0.7980 chunk 282 optimal weight: 9.9990 chunk 384 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 355 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 251 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.081789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.060424 restraints weight = 281783.942| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.74 r_work: 0.3114 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 34512 Z= 0.180 Angle : 0.790 59.175 47159 Z= 0.403 Chirality : 0.052 0.936 5573 Planarity : 0.005 0.072 5929 Dihedral : 5.425 61.126 4521 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.22 % Favored : 91.44 % Rotamer: Outliers : 0.90 % Allowed : 12.91 % Favored : 86.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.08 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.13), residues: 4193 helix: 1.46 (0.20), residues: 664 sheet: -0.83 (0.16), residues: 1022 loop : -1.82 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.021 0.001 TYR A 473 PHE 0.038 0.002 PHE C1052 TRP 0.036 0.002 TRP D 55 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (34384) covalent geometry : angle 0.75189 / 0.40 (46824) SS BOND : bond 0.00254 / 0.15 ( 48) SS BOND : angle 0.95707 / 0.69 ( 96) hydrogen bonds : bond 0.03650 / 2.41 ( 1117) hydrogen bonds : angle 5.50269 / 3.74 ( 3159) link_BETA1-4 : bond 0.00506 / 0.35 ( 29) link_BETA1-4 : angle 1.71670 / 1.21 ( 87) link_NAG-ASN : bond 0.00711 / 0.51 ( 50) link_NAG-ASN : angle 4.17628 / 2.75 ( 150) link_NAG-THR : bond 0.00190 / 0.10 ( 1) link_NAG-THR : angle 0.04568 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9805.40 seconds wall clock time: 168 minutes 48.27 seconds (10128.27 seconds total)