Starting phenix.real_space_refine on Fri Aug 7 10:59:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yib_72985/08_2026/9yib_72985.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yib_72985/08_2026/9yib_72985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yib_72985/08_2026/9yib_72985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yib_72985/08_2026/9yib_72985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yib_72985/08_2026/9yib_72985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yib_72985/08_2026/9yib_72985.map" } resolution = 4.3 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= 0.001 sd= 0.007 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 123 5.16 5 C 12882 2.51 5 N 3423 2.21 5 O 4200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20628 Number of models: 1 Model: "" Number of chains: 54 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1028 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "J" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1028 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "M" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1028 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.29, per 1000 atoms: 0.21 Number of scatterers: 20628 At special positions: 0 Unit cell: (159.744, 159.744, 133.12, 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 123 16.00 O 4200 8.00 N 3423 7.00 C 12882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA p 3 " - " MAN p 4 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA U 3 " - " MAN U 6 " " BMA d 3 " - " MAN d 5 " " BMA g 3 " - " MAN g 6 " " BMA p 3 " - " MAN p 5 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 637 " " NAG D 1 " - " ASN C 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 230 " " NAG E 604 " - " ASN E 241 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 344 " " NAG E 608 " - " ASN E 355 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 230 " " NAG F 604 " - " ASN F 241 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 344 " " NAG F 608 " - " ASN F 355 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 197 " " NAG G 603 " - " ASN G 230 " " NAG G 604 " - " ASN G 241 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 339 " " NAG G 607 " - " ASN G 344 " " NAG G 608 " - " ASN G 355 " " NAG I 1 " - " ASN G 88 " " NAG O 1 " - " ASN G 156 " " NAG P 1 " - " ASN G 160 " " NAG Q 1 " - " ASN G 234 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN G 276 " " NAG T 1 " - " ASN G 295 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 386 " " NAG W 1 " - " ASN G 392 " " NAG X 1 " - " ASN G 448 " " NAG Y 1 " - " ASN B 611 " " NAG Z 1 " - " ASN F 88 " " NAG a 1 " - " ASN F 156 " " NAG b 1 " - " ASN F 160 " " NAG c 1 " - " ASN F 234 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 332 " " NAG h 1 " - " ASN F 386 " " NAG i 1 " - " ASN F 392 " " NAG j 1 " - " ASN F 448 " " NAG k 1 " - " ASN A 611 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 156 " " NAG n 1 " - " ASN E 160 " " NAG o 1 " - " ASN E 234 " " NAG p 1 " - " ASN E 262 " " NAG q 1 " - " ASN E 276 " " NAG r 1 " - " ASN E 295 " " NAG s 1 " - " ASN E 332 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 782.6 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 20.4% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.895A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 Processing helix chain 'C' and resid 653 through 664 removed outlier: 4.090A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 97 removed outlier: 3.518A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.301A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.628A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.616A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.178A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.546A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.895A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 653 through 664 removed outlier: 4.091A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 97 removed outlier: 3.518A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 94 through 97' Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.302A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.629A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.617A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.178A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.546A pdb=" N ASP K 82 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.895A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 650 Processing helix chain 'A' and resid 653 through 664 removed outlier: 4.092A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 removed outlier: 3.518A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 94 through 97' Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.302A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.630A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.616A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.178A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.546A pdb=" N ASP N 82 " --> pdb=" O GLU N 79 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'C' and resid 603 through 604 removed outlier: 3.686A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.752A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.720A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'G' and resid 157 through 162 Processing sheet with id=AA7, first strand: chain 'G' and resid 259 through 261 Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AA9, first strand: chain 'G' and resid 300 through 307 removed outlier: 6.936A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N TYR H 100 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY G 324 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 331 through 334 Processing sheet with id=AB2, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.575A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.501A pdb=" N MET H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.662A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.749A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR H 90 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.502A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 603 through 604 removed outlier: 3.687A pdb=" N CYS B 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.752A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.720A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'F' and resid 157 through 162 Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 Processing sheet with id=AC8, first strand: chain 'F' and resid 271 through 274 Processing sheet with id=AC9, first strand: chain 'F' and resid 300 through 307 removed outlier: 6.937A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N TYR J 100 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY F 324 " --> pdb=" O TYR J 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AD2, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.575A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.501A pdb=" N MET J 12 " --> pdb=" O THR J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 20 through 21 removed outlier: 3.662A pdb=" N LEU J 80 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 58 through 59 removed outlier: 6.749A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER J 35 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR J 90 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.503A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 603 through 604 removed outlier: 3.686A pdb=" N CYS A 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.751A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AE4, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.720A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AE6, first strand: chain 'E' and resid 157 through 162 Processing sheet with id=AE7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AE8, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=AE9, first strand: chain 'E' and resid 300 through 307 removed outlier: 6.936A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N TYR M 100 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY E 324 " --> pdb=" O TYR M 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 331 through 334 Processing sheet with id=AF2, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.575A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AF4, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AF5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.502A pdb=" N MET M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'M' and resid 20 through 21 removed outlier: 3.662A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.750A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER M 35 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR M 90 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.502A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1602 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: 4.06 Time building geometry restraints manager: 2.63 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: 6417 1.34 - 1.46: 4097 1.46 - 1.58: 10375 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 21051 Sorted by residual: bond pdb=" C3 MAN g 4 " pdb=" O3 MAN g 4 " ideal model delta sigma weight residual 1.408 1.438 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 MAN g 6 " pdb=" O5 MAN g 6 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.438 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C2 BMA R 3 " pdb=" O2 BMA R 3 " ideal model delta sigma weight residual 1.402 1.432 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C3 MAN s 4 " pdb=" O3 MAN s 4 " ideal model delta sigma weight residual 1.408 1.438 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 21046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 27617 1.63 - 3.25: 850 3.25 - 4.88: 116 4.88 - 6.51: 22 6.51 - 8.13: 12 Bond angle restraints: 28617 Sorted by residual: angle pdb=" C1 BMA s 3 " pdb=" O5 BMA s 3 " pdb=" C5 BMA s 3 " ideal model delta sigma weight residual 118.82 110.69 8.13 3.00e+00 1.11e-01 7.35e+00 angle pdb=" C1 BMA U 3 " pdb=" O5 BMA U 3 " pdb=" C5 BMA U 3 " ideal model delta sigma weight residual 118.82 110.70 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" C1 BMA g 3 " pdb=" O5 BMA g 3 " pdb=" C5 BMA g 3 " ideal model delta sigma weight residual 118.82 110.72 8.10 3.00e+00 1.11e-01 7.28e+00 angle pdb=" C1 BMA R 3 " pdb=" O5 BMA R 3 " pdb=" C5 BMA R 3 " ideal model delta sigma weight residual 118.82 110.75 8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" C1 BMA p 3 " pdb=" O5 BMA p 3 " pdb=" C5 BMA p 3 " ideal model delta sigma weight residual 118.82 110.76 8.06 3.00e+00 1.11e-01 7.22e+00 ... (remaining 28612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 13304 24.43 - 48.86: 655 48.86 - 73.30: 102 73.30 - 97.73: 39 97.73 - 122.16: 93 Dihedral angle restraints: 14193 sinusoidal: 7254 harmonic: 6939 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual 93.00 154.70 -61.70 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual 93.00 154.68 -61.68 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual 93.00 154.66 -61.66 1 1.00e+01 1.00e-02 5.04e+01 ... (remaining 14190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 3543 1.014 - 2.027: 0 2.027 - 3.041: 0 3.041 - 4.055: 0 4.055 - 5.068: 18 Chirality restraints: 3561 Sorted by residual: chirality pdb=" C4 NAG F 601 " pdb=" C3 NAG F 601 " pdb=" C5 NAG F 601 " pdb=" O4 NAG F 601 " both_signs ideal model delta sigma weight residual False -2.53 2.54 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C4 NAG E 601 " pdb=" C3 NAG E 601 " pdb=" C5 NAG E 601 " pdb=" O4 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.53 2.53 -5.07 2.00e-01 2.50e+01 6.41e+02 chirality pdb=" C4 NAG G 601 " pdb=" C3 NAG G 601 " pdb=" C5 NAG G 601 " pdb=" O4 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.53 2.53 -5.06 2.00e-01 2.50e+01 6.41e+02 ... (remaining 3558 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN M 39 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO M 40 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN J 39 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO J 40 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO J 40 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 40 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 39 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO H 40 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " -0.016 5.00e-02 4.00e+02 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 8833 2.92 - 3.42: 19006 3.42 - 3.91: 33237 3.91 - 4.41: 35896 4.41 - 4.90: 60423 Nonbonded interactions: 157395 Sorted by model distance: nonbonded pdb=" NE ARG E 327 " pdb=" O TYR M 100A" model vdw 2.427 3.120 nonbonded pdb=" NE ARG F 327 " pdb=" O TYR J 100A" model vdw 2.427 3.120 nonbonded pdb=" NE ARG G 327 " pdb=" O TYR H 100A" model vdw 2.428 3.120 nonbonded pdb=" OD1 ASP E 325 " pdb=" CG ARG E 327 " model vdw 2.512 3.440 nonbonded pdb=" OD1 ASP G 325 " pdb=" CG ARG G 327 " model vdw 2.512 3.440 ... (remaining 157390 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' 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 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'R' selection = chain 'd' selection = chain 'p' } ncs_group { reference = chain 'U' selection = chain 'g' selection = chain 's' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.060 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: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.930 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21216 Z= 0.242 Angle : 0.670 8.617 29070 Z= 0.281 Chirality : 0.358 5.068 3561 Planarity : 0.003 0.028 3486 Dihedral : 18.020 122.158 9591 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2364 helix: 2.00 (0.28), residues: 408 sheet: 0.17 (0.22), residues: 609 loop : -1.23 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 100I TYR 0.014 0.001 TYR J 100 PHE 0.006 0.001 PHE G 159 TRP 0.006 0.001 TRP E 96 HIS 0.004 0.001 HIS F 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (21051) covalent geometry : angle 0.64504 / 0.27 (28617) SS BOND : bond 0.00167 / 0.10 ( 42) SS BOND : angle 0.45854 / 0.32 ( 84) hydrogen bonds : bond 0.14002 / 9.24 ( 621) hydrogen bonds : angle 6.18020 / 4.38 ( 1602) link_ALPHA1-3 : bond 0.00324 / 0.20 ( 9) link_ALPHA1-3 : angle 1.63541 / 1.15 ( 27) link_ALPHA1-6 : bond 0.00131 / 0.07 ( 6) link_ALPHA1-6 : angle 0.58436 / 0.34 ( 18) link_BETA1-4 : bond 0.00432 / 0.26 ( 42) link_BETA1-4 : angle 1.09131 / 0.78 ( 126) link_NAG-ASN : bond 0.00503 / 0.31 ( 66) link_NAG-ASN : angle 2.10659 / 1.46 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 GLN cc_start: 0.8662 (mp10) cc_final: 0.8069 (mp10) REVERT: C 543 ASN cc_start: 0.8456 (m-40) cc_final: 0.8218 (m110) REVERT: C 581 LEU cc_start: 0.8958 (tp) cc_final: 0.8564 (pp) REVERT: G 78 ASP cc_start: 0.7155 (p0) cc_final: 0.6942 (p0) REVERT: G 141 ASP cc_start: 0.6835 (p0) cc_final: 0.6316 (p0) REVERT: G 213 ILE cc_start: 0.8601 (pt) cc_final: 0.8167 (pt) REVERT: G 259 LEU cc_start: 0.9274 (mt) cc_final: 0.8922 (mt) REVERT: G 289 ASN cc_start: 0.9318 (p0) cc_final: 0.9093 (p0) REVERT: G 377 ASN cc_start: 0.8793 (t0) cc_final: 0.8410 (t0) REVERT: H 81 LYS cc_start: 0.6698 (tppt) cc_final: 0.6441 (tppp) REVERT: L 42 GLN cc_start: 0.7117 (mt0) cc_final: 0.6188 (mt0) REVERT: L 85 ILE cc_start: 0.7687 (mt) cc_final: 0.7383 (mp) REVERT: B 543 ASN cc_start: 0.8286 (m-40) cc_final: 0.7640 (m110) REVERT: B 588 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7966 (ttm-80) REVERT: B 638 TYR cc_start: 0.8409 (m-10) cc_final: 0.7598 (m-10) REVERT: B 639 THR cc_start: 0.8963 (p) cc_final: 0.8302 (p) REVERT: F 137 ASN cc_start: 0.8190 (p0) cc_final: 0.7507 (t0) REVERT: F 161 MET cc_start: 0.9409 (tpt) cc_final: 0.8890 (tpt) REVERT: F 377 ASN cc_start: 0.8806 (t0) cc_final: 0.8487 (t0) REVERT: J 73 THR cc_start: 0.5619 (p) cc_final: 0.5362 (p) REVERT: K 42 GLN cc_start: 0.6437 (mt0) cc_final: 0.5422 (mt0) REVERT: A 588 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8026 (ttm-80) REVERT: A 626 MET cc_start: 0.7323 (ttm) cc_final: 0.6010 (ttm) REVERT: A 638 TYR cc_start: 0.8380 (m-10) cc_final: 0.8093 (m-10) REVERT: E 47 ASP cc_start: 0.8108 (p0) cc_final: 0.7152 (p0) REVERT: E 137 ASN cc_start: 0.7835 (p0) cc_final: 0.7463 (t0) REVERT: E 141 ASP cc_start: 0.7463 (p0) cc_final: 0.7062 (p0) REVERT: E 467 THR cc_start: 0.8979 (m) cc_final: 0.8441 (m) REVERT: N 42 GLN cc_start: 0.6619 (mt0) cc_final: 0.5728 (mt0) REVERT: N 75 ILE cc_start: 0.8018 (mp) cc_final: 0.7744 (tp) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.1522 time to fit residues: 125.7113 Evaluate side-chains 321 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 577 GLN C 616 ASN C 630 GLN C 656 ASN G 33 ASN G 246 GLN G 258 GLN G 315 GLN G 330 HIS H 76 ASN L 38 GLN B 577 GLN B 630 GLN B 656 ASN F 33 ASN F 315 GLN F 330 HIS J 76 ASN A 543 ASN A 577 GLN A 630 GLN E 33 ASN E 246 GLN E 315 GLN E 330 HIS M 76 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.071989 restraints weight = 60627.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073801 restraints weight = 37194.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074996 restraints weight = 27067.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.075685 restraints weight = 22006.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.076250 restraints weight = 19367.232| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21216 Z= 0.149 Angle : 0.695 12.935 29070 Z= 0.312 Chirality : 0.048 0.360 3561 Planarity : 0.004 0.070 3486 Dihedral : 8.829 80.112 5121 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.28 % Allowed : 3.57 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2364 helix: 1.86 (0.28), residues: 408 sheet: 0.17 (0.22), residues: 585 loop : -1.20 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 100H TYR 0.031 0.002 TYR B 643 PHE 0.012 0.002 PHE N 32 TRP 0.012 0.001 TRP E 112 HIS 0.006 0.001 HIS F 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21051) covalent geometry : angle 0.63853 / 0.30 (28617) SS BOND : bond 0.00503 / 0.29 ( 42) SS BOND : angle 1.26782 / 0.78 ( 84) hydrogen bonds : bond 0.03075 / 2.03 ( 621) hydrogen bonds : angle 5.31882 / 3.80 ( 1602) link_ALPHA1-3 : bond 0.00470 / 0.28 ( 9) link_ALPHA1-3 : angle 2.85133 / 1.84 ( 27) link_ALPHA1-6 : bond 0.00551 / 0.30 ( 6) link_ALPHA1-6 : angle 2.04633 / 1.17 ( 18) link_BETA1-4 : bond 0.00385 / 0.23 ( 42) link_BETA1-4 : angle 1.77483 / 1.26 ( 126) link_NAG-ASN : bond 0.00665 / 0.41 ( 66) link_NAG-ASN : angle 2.80308 / 2.00 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 416 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 GLN cc_start: 0.8641 (mp10) cc_final: 0.8134 (mp10) REVERT: C 543 ASN cc_start: 0.8539 (m-40) cc_final: 0.8291 (m110) REVERT: C 630 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: G 140 ASN cc_start: 0.7347 (t0) cc_final: 0.7074 (t0) REVERT: G 141 ASP cc_start: 0.6888 (p0) cc_final: 0.6324 (p0) REVERT: G 289 ASN cc_start: 0.9331 (p0) cc_final: 0.9054 (p0) REVERT: L 75 ILE cc_start: 0.8660 (mp) cc_final: 0.8340 (mp) REVERT: B 543 ASN cc_start: 0.8097 (m-40) cc_final: 0.7877 (m110) REVERT: B 588 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7741 (ttm-80) REVERT: B 591 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8341 (pt0) REVERT: B 638 TYR cc_start: 0.8146 (m-10) cc_final: 0.7624 (m-10) REVERT: B 646 LEU cc_start: 0.8552 (tt) cc_final: 0.8049 (mt) REVERT: F 100 MET cc_start: 0.8820 (mtm) cc_final: 0.8589 (mtp) REVERT: F 137 ASN cc_start: 0.8260 (p0) cc_final: 0.7278 (t0) REVERT: F 161 MET cc_start: 0.9282 (tpt) cc_final: 0.8775 (tpt) REVERT: F 300 ASN cc_start: 0.8354 (p0) cc_final: 0.8140 (p0) REVERT: F 377 ASN cc_start: 0.8905 (t0) cc_final: 0.8553 (t0) REVERT: K 75 ILE cc_start: 0.8344 (mp) cc_final: 0.8142 (mp) REVERT: A 540 GLN cc_start: 0.8743 (mp10) cc_final: 0.8269 (mp10) REVERT: A 543 ASN cc_start: 0.8099 (m-40) cc_final: 0.7898 (m-40) REVERT: A 630 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: A 638 TYR cc_start: 0.8361 (m-10) cc_final: 0.8069 (m-10) REVERT: A 646 LEU cc_start: 0.8336 (tt) cc_final: 0.8004 (tt) REVERT: A 648 GLU cc_start: 0.8534 (pt0) cc_final: 0.8192 (pt0) REVERT: E 82 GLN cc_start: 0.7246 (mt0) cc_final: 0.6565 (mm110) REVERT: E 137 ASN cc_start: 0.8065 (p0) cc_final: 0.7323 (t0) REVERT: E 140 ASN cc_start: 0.7432 (t0) cc_final: 0.7227 (t0) REVERT: E 141 ASP cc_start: 0.7322 (p0) cc_final: 0.7035 (p0) REVERT: E 377 ASN cc_start: 0.8867 (t0) cc_final: 0.8651 (t0) REVERT: N 55 ASP cc_start: 0.7493 (m-30) cc_final: 0.7004 (m-30) REVERT: N 75 ILE cc_start: 0.8282 (mp) cc_final: 0.7631 (mp) outliers start: 6 outliers final: 1 residues processed: 422 average time/residue: 0.1441 time to fit residues: 93.0524 Evaluate side-chains 305 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 198 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 656 ASN G 302 ASN L 42 GLN B 656 ASN F 246 GLN E 258 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069120 restraints weight = 60981.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.070926 restraints weight = 37404.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072081 restraints weight = 27064.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072821 restraints weight = 22039.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073168 restraints weight = 19320.245| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21216 Z= 0.171 Angle : 0.657 11.618 29070 Z= 0.306 Chirality : 0.048 0.368 3561 Planarity : 0.004 0.069 3486 Dihedral : 8.194 68.566 5121 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.05 % Allowed : 4.08 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2364 helix: 1.60 (0.28), residues: 408 sheet: 0.04 (0.22), residues: 594 loop : -1.34 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 94 TYR 0.019 0.002 TYR H 100 PHE 0.016 0.002 PHE G 210 TRP 0.012 0.001 TRP G 427 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (21051) covalent geometry : angle 0.61185 / 0.30 (28617) SS BOND : bond 0.00587 / 0.30 ( 42) SS BOND : angle 1.19145 / 0.68 ( 84) hydrogen bonds : bond 0.03197 / 2.15 ( 621) hydrogen bonds : angle 5.18257 / 3.70 ( 1602) link_ALPHA1-3 : bond 0.00533 / 0.32 ( 9) link_ALPHA1-3 : angle 2.48541 / 1.64 ( 27) link_ALPHA1-6 : bond 0.00596 / 0.34 ( 6) link_ALPHA1-6 : angle 1.83358 / 1.06 ( 18) link_BETA1-4 : bond 0.00416 / 0.27 ( 42) link_BETA1-4 : angle 1.53779 / 1.09 ( 126) link_NAG-ASN : bond 0.00681 / 0.42 ( 66) link_NAG-ASN : angle 2.46916 / 1.72 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 GLN cc_start: 0.8558 (mp10) cc_final: 0.8089 (mp10) REVERT: C 543 ASN cc_start: 0.8601 (m-40) cc_final: 0.8320 (m110) REVERT: C 588 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7703 (ttm-80) REVERT: G 46 LYS cc_start: 0.8707 (tppt) cc_final: 0.8493 (tppt) REVERT: G 213 ILE cc_start: 0.8848 (pt) cc_final: 0.8528 (pt) REVERT: G 289 ASN cc_start: 0.9352 (p0) cc_final: 0.9112 (p0) REVERT: H 90 TYR cc_start: 0.8029 (m-80) cc_final: 0.7802 (m-80) REVERT: B 543 ASN cc_start: 0.8211 (m-40) cc_final: 0.7957 (m110) REVERT: B 590 GLN cc_start: 0.8801 (tp40) cc_final: 0.8586 (tp40) REVERT: B 591 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8507 (tt0) REVERT: B 638 TYR cc_start: 0.8295 (m-10) cc_final: 0.7822 (m-10) REVERT: B 648 GLU cc_start: 0.8534 (pt0) cc_final: 0.8204 (pt0) REVERT: F 53 PHE cc_start: 0.7675 (m-80) cc_final: 0.7471 (m-10) REVERT: F 100 MET cc_start: 0.8946 (mtm) cc_final: 0.8649 (mtp) REVERT: F 137 ASN cc_start: 0.8380 (p0) cc_final: 0.7568 (t0) REVERT: F 213 ILE cc_start: 0.8870 (pt) cc_final: 0.8668 (pt) REVERT: F 300 ASN cc_start: 0.8434 (p0) cc_final: 0.7925 (p0) REVERT: F 377 ASN cc_start: 0.9067 (t0) cc_final: 0.8641 (t0) REVERT: K 4 MET cc_start: 0.7711 (mmp) cc_final: 0.7400 (mmp) REVERT: K 82 ASP cc_start: 0.6826 (p0) cc_final: 0.6620 (p0) REVERT: A 540 GLN cc_start: 0.8648 (mp10) cc_final: 0.8243 (mp10) REVERT: A 626 MET cc_start: 0.8145 (ttm) cc_final: 0.7829 (ttm) REVERT: A 648 GLU cc_start: 0.8484 (pt0) cc_final: 0.8118 (pt0) REVERT: E 137 ASN cc_start: 0.8123 (p0) cc_final: 0.7403 (t0) REVERT: E 140 ASN cc_start: 0.7508 (t0) cc_final: 0.7272 (t0) REVERT: E 141 ASP cc_start: 0.7390 (p0) cc_final: 0.7055 (p0) REVERT: E 289 ASN cc_start: 0.9333 (p0) cc_final: 0.9131 (p0) REVERT: E 377 ASN cc_start: 0.8959 (t0) cc_final: 0.8690 (t0) REVERT: N 47 LEU cc_start: 0.7456 (mp) cc_final: 0.7094 (mp) REVERT: N 55 ASP cc_start: 0.7675 (m-30) cc_final: 0.7185 (m-30) outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.1482 time to fit residues: 89.1467 Evaluate side-chains 299 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 171 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 656 ASN G 302 ASN L 38 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN F 258 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070243 restraints weight = 61023.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072033 restraints weight = 37381.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073191 restraints weight = 27216.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073952 restraints weight = 22214.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.074356 restraints weight = 19466.307| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 21216 Z= 0.104 Angle : 0.617 10.798 29070 Z= 0.285 Chirality : 0.047 0.364 3561 Planarity : 0.003 0.061 3486 Dihedral : 7.567 60.423 5121 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2364 helix: 1.42 (0.28), residues: 411 sheet: 0.12 (0.22), residues: 594 loop : -1.34 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 94 TYR 0.019 0.001 TYR H 32 PHE 0.012 0.001 PHE K 71 TRP 0.010 0.001 TRP E 427 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (21051) covalent geometry : angle 0.57055 / 0.27 (28617) SS BOND : bond 0.00433 / 0.26 ( 42) SS BOND : angle 1.14359 / 0.69 ( 84) hydrogen bonds : bond 0.02898 / 1.92 ( 621) hydrogen bonds : angle 5.03411 / 3.58 ( 1602) link_ALPHA1-3 : bond 0.00633 / 0.38 ( 9) link_ALPHA1-3 : angle 2.55442 / 1.72 ( 27) link_ALPHA1-6 : bond 0.00605 / 0.35 ( 6) link_ALPHA1-6 : angle 1.93995 / 1.12 ( 18) link_BETA1-4 : bond 0.00426 / 0.26 ( 42) link_BETA1-4 : angle 1.51553 / 1.07 ( 126) link_NAG-ASN : bond 0.00526 / 0.32 ( 66) link_NAG-ASN : angle 2.36158 / 1.67 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8607 (m-40) cc_final: 0.8391 (m110) REVERT: C 588 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7661 (ttm-80) REVERT: C 632 ASP cc_start: 0.8815 (t70) cc_final: 0.8556 (t0) REVERT: C 638 TYR cc_start: 0.8375 (m-10) cc_final: 0.8145 (m-10) REVERT: G 46 LYS cc_start: 0.8737 (tppt) cc_final: 0.8528 (tppt) REVERT: G 67 ASN cc_start: 0.9467 (t0) cc_final: 0.9260 (t0) REVERT: G 100 MET cc_start: 0.8546 (mtp) cc_final: 0.8338 (mtp) REVERT: G 259 LEU cc_start: 0.9337 (mt) cc_final: 0.9055 (mp) REVERT: H 3 GLN cc_start: 0.6036 (pp30) cc_final: 0.5573 (pp30) REVERT: L 65 THR cc_start: 0.7831 (p) cc_final: 0.7584 (p) REVERT: B 543 ASN cc_start: 0.8242 (m-40) cc_final: 0.8028 (m110) REVERT: B 590 GLN cc_start: 0.8798 (tp40) cc_final: 0.8520 (tp40) REVERT: B 638 TYR cc_start: 0.8214 (m-10) cc_final: 0.7790 (m-10) REVERT: B 648 GLU cc_start: 0.8449 (pt0) cc_final: 0.8101 (pt0) REVERT: F 137 ASN cc_start: 0.8357 (p0) cc_final: 0.7503 (t0) REVERT: F 289 ASN cc_start: 0.9289 (p0) cc_final: 0.8959 (p0) REVERT: F 377 ASN cc_start: 0.8978 (t0) cc_final: 0.8577 (t0) REVERT: F 427 TRP cc_start: 0.8164 (m-10) cc_final: 0.7914 (m-90) REVERT: K 73 LEU cc_start: 0.8391 (tt) cc_final: 0.8032 (tt) REVERT: K 98 PHE cc_start: 0.7308 (m-80) cc_final: 0.6590 (p90) REVERT: A 540 GLN cc_start: 0.8518 (mp10) cc_final: 0.8020 (mp10) REVERT: A 638 TYR cc_start: 0.8387 (m-10) cc_final: 0.8106 (m-10) REVERT: A 648 GLU cc_start: 0.8546 (pt0) cc_final: 0.8260 (pt0) REVERT: E 53 PHE cc_start: 0.7807 (m-80) cc_final: 0.7603 (m-80) REVERT: E 137 ASN cc_start: 0.8125 (p0) cc_final: 0.7368 (t0) REVERT: E 141 ASP cc_start: 0.7227 (p0) cc_final: 0.7011 (p0) REVERT: E 289 ASN cc_start: 0.9335 (p0) cc_final: 0.9112 (p0) REVERT: E 377 ASN cc_start: 0.8920 (t0) cc_final: 0.8682 (t0) REVERT: M 100 PHE cc_start: 0.7819 (m-80) cc_final: 0.7318 (m-80) REVERT: N 55 ASP cc_start: 0.7679 (m-30) cc_final: 0.7115 (m-30) outliers start: 1 outliers final: 0 residues processed: 400 average time/residue: 0.1448 time to fit residues: 88.7391 Evaluate side-chains 296 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 107 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 139 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN G 302 ASN L 38 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** N 100 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 = 0.3402 r_free = 0.3402 target = 0.088677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.067462 restraints weight = 61238.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.069211 restraints weight = 37326.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.070338 restraints weight = 27155.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071023 restraints weight = 22169.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.071488 restraints weight = 19596.591| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21216 Z= 0.160 Angle : 0.675 13.595 29070 Z= 0.311 Chirality : 0.048 0.343 3561 Planarity : 0.004 0.059 3486 Dihedral : 7.359 59.975 5121 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2364 helix: 1.50 (0.28), residues: 381 sheet: -0.02 (0.22), residues: 612 loop : -1.16 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 94 TYR 0.022 0.001 TYR L 49 PHE 0.014 0.001 PHE L 62 TRP 0.028 0.001 TRP H 7 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (21051) covalent geometry : angle 0.62538 / 0.30 (28617) SS BOND : bond 0.00465 / 0.27 ( 42) SS BOND : angle 1.16912 / 0.71 ( 84) hydrogen bonds : bond 0.03135 / 2.08 ( 621) hydrogen bonds : angle 5.09367 / 3.64 ( 1602) link_ALPHA1-3 : bond 0.00553 / 0.33 ( 9) link_ALPHA1-3 : angle 2.57528 / 1.72 ( 27) link_ALPHA1-6 : bond 0.00493 / 0.28 ( 6) link_ALPHA1-6 : angle 2.08447 / 1.19 ( 18) link_BETA1-4 : bond 0.00431 / 0.28 ( 42) link_BETA1-4 : angle 1.61790 / 1.14 ( 126) link_NAG-ASN : bond 0.00561 / 0.33 ( 66) link_NAG-ASN : angle 2.59426 / 1.84 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 383 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 588 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7789 (ttm-80) REVERT: C 632 ASP cc_start: 0.8724 (t70) cc_final: 0.8476 (t0) REVERT: C 638 TYR cc_start: 0.8386 (m-10) cc_final: 0.8175 (m-10) REVERT: G 213 ILE cc_start: 0.8977 (pt) cc_final: 0.8758 (pt) REVERT: G 259 LEU cc_start: 0.9399 (mt) cc_final: 0.9151 (mt) REVERT: G 289 ASN cc_start: 0.9350 (p0) cc_final: 0.9136 (p0) REVERT: H 3 GLN cc_start: 0.6058 (pp30) cc_final: 0.5268 (pp30) REVERT: H 5 GLN cc_start: 0.6705 (pm20) cc_final: 0.5036 (pm20) REVERT: B 543 ASN cc_start: 0.8314 (m-40) cc_final: 0.7980 (m110) REVERT: B 638 TYR cc_start: 0.8289 (m-10) cc_final: 0.7915 (m-10) REVERT: F 137 ASN cc_start: 0.8428 (p0) cc_final: 0.7529 (t0) REVERT: F 140 ASN cc_start: 0.7581 (p0) cc_final: 0.6747 (t0) REVERT: F 141 ASP cc_start: 0.7023 (p0) cc_final: 0.6566 (p0) REVERT: F 289 ASN cc_start: 0.9300 (p0) cc_final: 0.8946 (p0) REVERT: F 377 ASN cc_start: 0.9039 (t0) cc_final: 0.8641 (t0) REVERT: J 36 TRP cc_start: 0.6087 (m100) cc_final: 0.5314 (m100) REVERT: K 42 GLN cc_start: 0.5834 (pm20) cc_final: 0.5194 (pm20) REVERT: K 98 PHE cc_start: 0.7450 (m-80) cc_final: 0.7192 (m-80) REVERT: A 540 GLN cc_start: 0.8616 (mp10) cc_final: 0.8082 (mp10) REVERT: A 543 ASN cc_start: 0.8298 (m110) cc_final: 0.7930 (m110) REVERT: A 638 TYR cc_start: 0.8375 (m-10) cc_final: 0.8091 (m-10) REVERT: E 137 ASN cc_start: 0.8131 (p0) cc_final: 0.7373 (t0) REVERT: E 289 ASN cc_start: 0.9361 (p0) cc_final: 0.9141 (p0) REVERT: E 377 ASN cc_start: 0.8956 (t0) cc_final: 0.8706 (t0) REVERT: N 47 LEU cc_start: 0.7829 (mp) cc_final: 0.7321 (mp) REVERT: N 55 ASP cc_start: 0.7752 (m-30) cc_final: 0.7254 (m-30) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.1372 time to fit residues: 81.1765 Evaluate side-chains 299 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 148 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 656 ASN G 302 ASN E 302 ASN ** N 100 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 = 0.3384 r_free = 0.3384 target = 0.087787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.066811 restraints weight = 60861.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068553 restraints weight = 36855.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069681 restraints weight = 26680.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070386 restraints weight = 21742.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070804 restraints weight = 19128.655| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21216 Z= 0.141 Angle : 0.651 9.941 29070 Z= 0.303 Chirality : 0.047 0.337 3561 Planarity : 0.004 0.057 3486 Dihedral : 6.517 58.798 5121 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2364 helix: 1.41 (0.28), residues: 381 sheet: 0.14 (0.23), residues: 582 loop : -1.20 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 30 TYR 0.023 0.001 TYR N 49 PHE 0.013 0.001 PHE J 78 TRP 0.013 0.001 TRP M 36 HIS 0.003 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (21051) covalent geometry : angle 0.60569 / 0.29 (28617) SS BOND : bond 0.00431 / 0.26 ( 42) SS BOND : angle 1.14532 / 0.70 ( 84) hydrogen bonds : bond 0.03076 / 2.02 ( 621) hydrogen bonds : angle 5.08010 / 3.65 ( 1602) link_ALPHA1-3 : bond 0.00595 / 0.38 ( 9) link_ALPHA1-3 : angle 2.58071 / 1.75 ( 27) link_ALPHA1-6 : bond 0.00352 / 0.20 ( 6) link_ALPHA1-6 : angle 1.97306 / 1.17 ( 18) link_BETA1-4 : bond 0.00447 / 0.29 ( 42) link_BETA1-4 : angle 1.60467 / 1.13 ( 126) link_NAG-ASN : bond 0.00511 / 0.31 ( 66) link_NAG-ASN : angle 2.39783 / 1.68 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8632 (m110) cc_final: 0.8290 (m110) REVERT: C 588 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7840 (ttm-80) REVERT: C 632 ASP cc_start: 0.8714 (t70) cc_final: 0.8468 (t0) REVERT: C 638 TYR cc_start: 0.8449 (m-10) cc_final: 0.8193 (m-10) REVERT: G 67 ASN cc_start: 0.9490 (t0) cc_final: 0.9240 (t0) REVERT: G 140 ASN cc_start: 0.7333 (t0) cc_final: 0.6759 (t0) REVERT: G 289 ASN cc_start: 0.9346 (p0) cc_final: 0.9123 (p0) REVERT: L 65 THR cc_start: 0.8223 (t) cc_final: 0.8005 (p) REVERT: B 543 ASN cc_start: 0.8321 (m-40) cc_final: 0.8021 (m110) REVERT: B 638 TYR cc_start: 0.8322 (m-10) cc_final: 0.7978 (m-10) REVERT: F 137 ASN cc_start: 0.8478 (p0) cc_final: 0.7623 (t0) REVERT: F 140 ASN cc_start: 0.7709 (p0) cc_final: 0.6911 (t0) REVERT: F 141 ASP cc_start: 0.6877 (p0) cc_final: 0.6530 (p0) REVERT: F 161 MET cc_start: 0.9018 (tpp) cc_final: 0.7732 (tpt) REVERT: F 289 ASN cc_start: 0.9291 (p0) cc_final: 0.8916 (p0) REVERT: F 297 THR cc_start: 0.8205 (m) cc_final: 0.7987 (p) REVERT: J 36 TRP cc_start: 0.6465 (m100) cc_final: 0.5772 (m100) REVERT: J 94 ARG cc_start: 0.8365 (ttt90) cc_final: 0.8037 (ttm-80) REVERT: K 94 TRP cc_start: 0.8150 (m100) cc_final: 0.7874 (m100) REVERT: A 540 GLN cc_start: 0.8662 (mp10) cc_final: 0.8211 (mp10) REVERT: A 543 ASN cc_start: 0.8360 (m110) cc_final: 0.7993 (m110) REVERT: A 638 TYR cc_start: 0.8388 (m-10) cc_final: 0.8077 (m-10) REVERT: E 137 ASN cc_start: 0.8254 (p0) cc_final: 0.7509 (t0) REVERT: E 289 ASN cc_start: 0.9396 (p0) cc_final: 0.9185 (p0) REVERT: E 377 ASN cc_start: 0.8930 (t0) cc_final: 0.8675 (t0) REVERT: N 47 LEU cc_start: 0.7846 (mp) cc_final: 0.7392 (mp) REVERT: N 55 ASP cc_start: 0.7890 (m-30) cc_final: 0.7334 (m-30) outliers start: 2 outliers final: 0 residues processed: 372 average time/residue: 0.1337 time to fit residues: 76.0582 Evaluate side-chains 293 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 202 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN K 93 HIS E 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066720 restraints weight = 61244.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068490 restraints weight = 36845.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069618 restraints weight = 26647.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.070338 restraints weight = 21741.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070807 restraints weight = 19109.946| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21216 Z= 0.125 Angle : 0.643 9.371 29070 Z= 0.297 Chirality : 0.047 0.338 3561 Planarity : 0.003 0.057 3486 Dihedral : 6.114 58.345 5121 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.09 % Allowed : 1.41 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2364 helix: 1.48 (0.29), residues: 378 sheet: 0.12 (0.23), residues: 570 loop : -1.15 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 94 TYR 0.027 0.001 TYR N 49 PHE 0.012 0.001 PHE H 78 TRP 0.016 0.001 TRP H 7 HIS 0.002 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (21051) covalent geometry : angle 0.59753 / 0.29 (28617) SS BOND : bond 0.00404 / 0.24 ( 42) SS BOND : angle 1.22082 / 0.77 ( 84) hydrogen bonds : bond 0.02973 / 1.97 ( 621) hydrogen bonds : angle 5.02440 / 3.61 ( 1602) link_ALPHA1-3 : bond 0.00542 / 0.34 ( 9) link_ALPHA1-3 : angle 2.50018 / 1.69 ( 27) link_ALPHA1-6 : bond 0.00119 / 0.06 ( 6) link_ALPHA1-6 : angle 1.91223 / 1.08 ( 18) link_BETA1-4 : bond 0.00447 / 0.28 ( 42) link_BETA1-4 : angle 1.59168 / 1.12 ( 126) link_NAG-ASN : bond 0.00519 / 0.32 ( 66) link_NAG-ASN : angle 2.37409 / 1.66 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8690 (m110) cc_final: 0.8273 (m110) REVERT: C 588 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7776 (ttm-80) REVERT: C 632 ASP cc_start: 0.8694 (t70) cc_final: 0.8443 (t0) REVERT: C 638 TYR cc_start: 0.8448 (m-10) cc_final: 0.8215 (m-10) REVERT: G 46 LYS cc_start: 0.8855 (tppt) cc_final: 0.8592 (tppt) REVERT: G 53 PHE cc_start: 0.7881 (m-80) cc_final: 0.7665 (m-10) REVERT: G 140 ASN cc_start: 0.7453 (t0) cc_final: 0.6997 (t0) REVERT: G 161 MET cc_start: 0.9105 (tpp) cc_final: 0.8237 (tpt) REVERT: G 259 LEU cc_start: 0.9389 (mt) cc_final: 0.9124 (mp) REVERT: G 289 ASN cc_start: 0.9360 (p0) cc_final: 0.9099 (p0) REVERT: L 42 GLN cc_start: 0.6109 (mt0) cc_final: 0.5713 (mp10) REVERT: B 543 ASN cc_start: 0.8280 (m-40) cc_final: 0.7986 (m110) REVERT: B 638 TYR cc_start: 0.8354 (m-10) cc_final: 0.8015 (m-10) REVERT: F 137 ASN cc_start: 0.8510 (p0) cc_final: 0.7664 (t0) REVERT: F 140 ASN cc_start: 0.7723 (p0) cc_final: 0.6905 (t0) REVERT: F 141 ASP cc_start: 0.6827 (p0) cc_final: 0.6517 (p0) REVERT: F 161 MET cc_start: 0.9055 (tpp) cc_final: 0.7654 (tpt) REVERT: F 289 ASN cc_start: 0.9261 (p0) cc_final: 0.8910 (p0) REVERT: F 297 THR cc_start: 0.8255 (m) cc_final: 0.8043 (p) REVERT: J 36 TRP cc_start: 0.6444 (m100) cc_final: 0.6001 (m100) REVERT: K 39 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7499 (mtpt) REVERT: K 94 TRP cc_start: 0.8139 (m100) cc_final: 0.7926 (m100) REVERT: K 98 PHE cc_start: 0.7600 (m-80) cc_final: 0.7236 (m-80) REVERT: A 540 GLN cc_start: 0.8736 (mp10) cc_final: 0.8221 (mp10) REVERT: A 543 ASN cc_start: 0.8358 (m110) cc_final: 0.7975 (m110) REVERT: A 648 GLU cc_start: 0.8478 (pt0) cc_final: 0.8177 (pt0) REVERT: E 53 PHE cc_start: 0.7950 (m-80) cc_final: 0.7738 (m-80) REVERT: E 137 ASN cc_start: 0.8272 (p0) cc_final: 0.7546 (t0) REVERT: E 259 LEU cc_start: 0.9406 (mt) cc_final: 0.9043 (mt) REVERT: E 289 ASN cc_start: 0.9397 (p0) cc_final: 0.9172 (p0) REVERT: E 377 ASN cc_start: 0.8903 (t0) cc_final: 0.8650 (t0) REVERT: N 36 TYR cc_start: 0.8165 (m-80) cc_final: 0.7940 (m-80) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.1337 time to fit residues: 78.0491 Evaluate side-chains 312 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 52 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN E 302 ASN ** N 100 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 = 0.3295 r_free = 0.3295 target = 0.083084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.062297 restraints weight = 61985.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064005 restraints weight = 37511.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065094 restraints weight = 27252.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.065719 restraints weight = 22354.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066191 restraints weight = 19815.709| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21216 Z= 0.228 Angle : 0.751 9.878 29070 Z= 0.353 Chirality : 0.049 0.348 3561 Planarity : 0.004 0.059 3486 Dihedral : 6.600 58.481 5121 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.14 % Allowed : 1.27 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2364 helix: 0.76 (0.28), residues: 396 sheet: -0.14 (0.23), residues: 567 loop : -1.17 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 143 TYR 0.028 0.002 TYR H 32 PHE 0.023 0.002 PHE J 78 TRP 0.021 0.002 TRP J 103 HIS 0.004 0.001 HIS F 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (21051) covalent geometry : angle 0.70254 / 0.34 (28617) SS BOND : bond 0.00624 / 0.35 ( 42) SS BOND : angle 1.53479 / 0.98 ( 84) hydrogen bonds : bond 0.03554 / 2.34 ( 621) hydrogen bonds : angle 5.39200 / 3.88 ( 1602) link_ALPHA1-3 : bond 0.00408 / 0.23 ( 9) link_ALPHA1-3 : angle 2.75607 / 1.87 ( 27) link_ALPHA1-6 : bond 0.00375 / 0.19 ( 6) link_ALPHA1-6 : angle 2.11415 / 1.17 ( 18) link_BETA1-4 : bond 0.00440 / 0.28 ( 42) link_BETA1-4 : angle 1.78727 / 1.25 ( 126) link_NAG-ASN : bond 0.00587 / 0.36 ( 66) link_NAG-ASN : angle 2.63252 / 1.83 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 371 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8681 (m110) cc_final: 0.8245 (m110) REVERT: C 588 ARG cc_start: 0.8191 (ttm170) cc_final: 0.7903 (ttm-80) REVERT: C 626 MET cc_start: 0.7483 (ttm) cc_final: 0.7159 (ttm) REVERT: C 632 ASP cc_start: 0.8781 (t70) cc_final: 0.8525 (t0) REVERT: C 638 TYR cc_start: 0.8497 (m-10) cc_final: 0.8266 (m-10) REVERT: C 656 ASN cc_start: 0.7737 (m-40) cc_final: 0.7287 (p0) REVERT: G 42 VAL cc_start: 0.8949 (t) cc_final: 0.8725 (p) REVERT: G 53 PHE cc_start: 0.8103 (m-80) cc_final: 0.7847 (m-10) REVERT: G 140 ASN cc_start: 0.7551 (t0) cc_final: 0.7112 (t0) REVERT: G 161 MET cc_start: 0.9047 (tpp) cc_final: 0.8361 (tpt) REVERT: G 289 ASN cc_start: 0.9363 (p0) cc_final: 0.9055 (p0) REVERT: G 297 THR cc_start: 0.8610 (m) cc_final: 0.8343 (p) REVERT: H 5 GLN cc_start: 0.7093 (mp10) cc_final: 0.6615 (mp10) REVERT: L 42 GLN cc_start: 0.6079 (mt0) cc_final: 0.5862 (mp10) REVERT: B 543 ASN cc_start: 0.8429 (m-40) cc_final: 0.8065 (m110) REVERT: B 638 TYR cc_start: 0.8360 (m-10) cc_final: 0.8010 (m-10) REVERT: F 103 GLN cc_start: 0.7911 (tp40) cc_final: 0.7667 (tm-30) REVERT: F 137 ASN cc_start: 0.8595 (p0) cc_final: 0.7760 (t0) REVERT: F 140 ASN cc_start: 0.7779 (p0) cc_final: 0.6912 (t0) REVERT: F 141 ASP cc_start: 0.6970 (p0) cc_final: 0.6667 (p0) REVERT: F 161 MET cc_start: 0.9033 (tpp) cc_final: 0.8592 (tpt) REVERT: F 297 THR cc_start: 0.8784 (m) cc_final: 0.8480 (p) REVERT: J 36 TRP cc_start: 0.6947 (m100) cc_final: 0.6370 (m100) REVERT: K 39 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7477 (mtpt) REVERT: K 55 ASP cc_start: 0.8285 (t70) cc_final: 0.8024 (t0) REVERT: K 94 TRP cc_start: 0.8240 (m100) cc_final: 0.8020 (m100) REVERT: A 540 GLN cc_start: 0.8717 (mp10) cc_final: 0.8201 (mp10) REVERT: A 543 ASN cc_start: 0.8465 (m110) cc_final: 0.8026 (m110) REVERT: E 137 ASN cc_start: 0.8448 (p0) cc_final: 0.7705 (t0) REVERT: E 289 ASN cc_start: 0.9418 (p0) cc_final: 0.9170 (p0) REVERT: E 377 ASN cc_start: 0.8966 (t0) cc_final: 0.8713 (t0) REVERT: N 36 TYR cc_start: 0.8200 (m-80) cc_final: 0.7929 (m-80) REVERT: N 47 LEU cc_start: 0.8189 (mp) cc_final: 0.7921 (mp) REVERT: N 55 ASP cc_start: 0.8185 (t70) cc_final: 0.7897 (t70) REVERT: N 85 ILE cc_start: 0.7829 (mp) cc_final: 0.7390 (mp) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.1634 time to fit residues: 93.2494 Evaluate side-chains 295 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 95 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 139 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN G 302 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** N 100 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 = 0.3346 r_free = 0.3346 target = 0.085687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.065115 restraints weight = 61120.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.066879 restraints weight = 36671.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068016 restraints weight = 26373.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068740 restraints weight = 21435.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.069205 restraints weight = 18767.890| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21216 Z= 0.118 Angle : 0.668 9.379 29070 Z= 0.312 Chirality : 0.049 0.421 3561 Planarity : 0.004 0.062 3486 Dihedral : 6.036 57.305 5121 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2364 helix: 0.85 (0.28), residues: 399 sheet: -0.12 (0.23), residues: 576 loop : -1.16 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 94 TYR 0.018 0.001 TYR H 32 PHE 0.013 0.001 PHE J 78 TRP 0.017 0.001 TRP H 7 HIS 0.002 0.000 HIS N 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21051) covalent geometry : angle 0.62475 / 0.30 (28617) SS BOND : bond 0.00415 / 0.23 ( 42) SS BOND : angle 1.07199 / 0.66 ( 84) hydrogen bonds : bond 0.03158 / 2.08 ( 621) hydrogen bonds : angle 5.13774 / 3.72 ( 1602) link_ALPHA1-3 : bond 0.00495 / 0.29 ( 9) link_ALPHA1-3 : angle 2.53152 / 1.74 ( 27) link_ALPHA1-6 : bond 0.00090 / 0.05 ( 6) link_ALPHA1-6 : angle 1.81965 / 1.02 ( 18) link_BETA1-4 : bond 0.00430 / 0.27 ( 42) link_BETA1-4 : angle 1.61475 / 1.14 ( 126) link_NAG-ASN : bond 0.00490 / 0.30 ( 66) link_NAG-ASN : angle 2.38849 / 1.66 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8698 (m110) cc_final: 0.8370 (m110) REVERT: C 588 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7933 (ttm-80) REVERT: C 626 MET cc_start: 0.7686 (ttm) cc_final: 0.7365 (ttm) REVERT: C 632 ASP cc_start: 0.8709 (t70) cc_final: 0.8422 (t0) REVERT: C 638 TYR cc_start: 0.8360 (m-10) cc_final: 0.8086 (m-10) REVERT: C 656 ASN cc_start: 0.7791 (m-40) cc_final: 0.7341 (p0) REVERT: G 140 ASN cc_start: 0.7446 (t0) cc_final: 0.7156 (t0) REVERT: G 161 MET cc_start: 0.9053 (tpp) cc_final: 0.8388 (tpt) REVERT: G 289 ASN cc_start: 0.9337 (p0) cc_final: 0.9054 (p0) REVERT: G 297 THR cc_start: 0.8520 (m) cc_final: 0.8218 (p) REVERT: H 5 GLN cc_start: 0.7312 (mp10) cc_final: 0.6813 (mp10) REVERT: H 100 TYR cc_start: 0.7504 (p90) cc_final: 0.7288 (p90) REVERT: B 543 ASN cc_start: 0.8329 (m-40) cc_final: 0.8075 (m110) REVERT: B 632 ASP cc_start: 0.8759 (t70) cc_final: 0.8556 (t0) REVERT: B 638 TYR cc_start: 0.8296 (m-10) cc_final: 0.7939 (m-10) REVERT: F 100 MET cc_start: 0.8856 (mtp) cc_final: 0.8398 (mtp) REVERT: F 137 ASN cc_start: 0.8567 (p0) cc_final: 0.7772 (t0) REVERT: F 140 ASN cc_start: 0.7713 (p0) cc_final: 0.6865 (t0) REVERT: F 141 ASP cc_start: 0.6768 (p0) cc_final: 0.6480 (p0) REVERT: F 161 MET cc_start: 0.9046 (tpp) cc_final: 0.7449 (tpt) REVERT: F 297 THR cc_start: 0.8670 (m) cc_final: 0.8381 (p) REVERT: J 36 TRP cc_start: 0.6870 (m100) cc_final: 0.6249 (m100) REVERT: K 55 ASP cc_start: 0.8269 (t70) cc_final: 0.7948 (t70) REVERT: A 540 GLN cc_start: 0.8766 (mp10) cc_final: 0.8248 (mp10) REVERT: A 543 ASN cc_start: 0.8417 (m110) cc_final: 0.7988 (m110) REVERT: E 137 ASN cc_start: 0.8365 (p0) cc_final: 0.7623 (t0) REVERT: E 289 ASN cc_start: 0.9350 (p0) cc_final: 0.9109 (p0) REVERT: E 377 ASN cc_start: 0.8846 (t0) cc_final: 0.8581 (t0) REVERT: N 36 TYR cc_start: 0.8109 (m-80) cc_final: 0.7826 (m-80) REVERT: N 94 TRP cc_start: 0.8265 (m100) cc_final: 0.8059 (m100) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.1620 time to fit residues: 91.9648 Evaluate side-chains 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 118 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN E 302 ASN N 27 HIS ** N 100 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 = 0.3338 r_free = 0.3338 target = 0.085292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.064805 restraints weight = 61431.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.066560 restraints weight = 36671.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.067685 restraints weight = 26323.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.068377 restraints weight = 21372.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068782 restraints weight = 18783.449| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21216 Z= 0.123 Angle : 0.676 13.840 29070 Z= 0.313 Chirality : 0.048 0.347 3561 Planarity : 0.004 0.064 3486 Dihedral : 5.862 57.480 5121 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2364 helix: 1.17 (0.29), residues: 381 sheet: -0.06 (0.23), residues: 570 loop : -1.18 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 94 TYR 0.018 0.001 TYR H 32 PHE 0.013 0.001 PHE J 78 TRP 0.023 0.001 TRP H 47 HIS 0.003 0.001 HIS K 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (21051) covalent geometry : angle 0.63297 / 0.30 (28617) SS BOND : bond 0.00409 / 0.23 ( 42) SS BOND : angle 1.03532 / 0.64 ( 84) hydrogen bonds : bond 0.03097 / 2.03 ( 621) hydrogen bonds : angle 5.12688 / 3.71 ( 1602) link_ALPHA1-3 : bond 0.00394 / 0.24 ( 9) link_ALPHA1-3 : angle 2.49427 / 1.72 ( 27) link_ALPHA1-6 : bond 0.00060 / 0.03 ( 6) link_ALPHA1-6 : angle 1.76461 / 0.98 ( 18) link_BETA1-4 : bond 0.00432 / 0.27 ( 42) link_BETA1-4 : angle 1.63501 / 1.15 ( 126) link_NAG-ASN : bond 0.00559 / 0.34 ( 66) link_NAG-ASN : angle 2.42233 / 1.67 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8726 (m110) cc_final: 0.8380 (m110) REVERT: C 588 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7902 (ttm-80) REVERT: C 626 MET cc_start: 0.7734 (ttm) cc_final: 0.7402 (ttm) REVERT: C 632 ASP cc_start: 0.8687 (t70) cc_final: 0.8378 (t0) REVERT: C 638 TYR cc_start: 0.8349 (m-10) cc_final: 0.8074 (m-10) REVERT: C 656 ASN cc_start: 0.7964 (m-40) cc_final: 0.7422 (p0) REVERT: G 140 ASN cc_start: 0.7396 (t0) cc_final: 0.7184 (t0) REVERT: G 161 MET cc_start: 0.9054 (tpp) cc_final: 0.8405 (tpt) REVERT: G 289 ASN cc_start: 0.9329 (p0) cc_final: 0.9064 (p0) REVERT: G 297 THR cc_start: 0.8517 (m) cc_final: 0.8271 (p) REVERT: H 5 GLN cc_start: 0.7361 (mp10) cc_final: 0.6507 (mp10) REVERT: H 86 ASP cc_start: 0.6695 (m-30) cc_final: 0.6450 (m-30) REVERT: H 100 TYR cc_start: 0.7605 (p90) cc_final: 0.7341 (p90) REVERT: B 543 ASN cc_start: 0.8360 (m-40) cc_final: 0.8063 (m110) REVERT: B 632 ASP cc_start: 0.8784 (t70) cc_final: 0.8559 (t0) REVERT: B 638 TYR cc_start: 0.8284 (m-10) cc_final: 0.7943 (m-10) REVERT: F 100 MET cc_start: 0.8789 (mtp) cc_final: 0.8255 (mtp) REVERT: F 137 ASN cc_start: 0.8575 (p0) cc_final: 0.7794 (t0) REVERT: F 140 ASN cc_start: 0.7719 (p0) cc_final: 0.6859 (t0) REVERT: F 141 ASP cc_start: 0.6693 (p0) cc_final: 0.6381 (p0) REVERT: F 161 MET cc_start: 0.9069 (tpp) cc_final: 0.7804 (tpt) REVERT: F 297 THR cc_start: 0.8676 (m) cc_final: 0.8419 (p) REVERT: J 36 TRP cc_start: 0.6911 (m100) cc_final: 0.6266 (m100) REVERT: K 60 ASP cc_start: 0.8470 (p0) cc_final: 0.8173 (p0) REVERT: A 540 GLN cc_start: 0.8776 (mp10) cc_final: 0.8302 (mp10) REVERT: A 543 ASN cc_start: 0.8432 (m110) cc_final: 0.7980 (m110) REVERT: A 648 GLU cc_start: 0.8398 (pt0) cc_final: 0.8072 (pt0) REVERT: E 46 LYS cc_start: 0.9016 (tppt) cc_final: 0.8429 (tppt) REVERT: E 137 ASN cc_start: 0.8394 (p0) cc_final: 0.7666 (t0) REVERT: E 259 LEU cc_start: 0.9171 (mp) cc_final: 0.8967 (mm) REVERT: E 289 ASN cc_start: 0.9349 (p0) cc_final: 0.9114 (p0) REVERT: E 377 ASN cc_start: 0.8823 (t0) cc_final: 0.8570 (t0) outliers start: 2 outliers final: 0 residues processed: 373 average time/residue: 0.1636 time to fit residues: 93.4487 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 203 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** N 100 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 = 0.3331 r_free = 0.3331 target = 0.084918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064448 restraints weight = 61405.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066197 restraints weight = 36817.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.067310 restraints weight = 26569.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068046 restraints weight = 21610.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068447 restraints weight = 18946.357| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21216 Z= 0.129 Angle : 0.674 12.421 29070 Z= 0.314 Chirality : 0.048 0.337 3561 Planarity : 0.004 0.064 3486 Dihedral : 5.764 57.292 5121 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2364 helix: 1.11 (0.29), residues: 381 sheet: 0.02 (0.22), residues: 582 loop : -1.21 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 94 TYR 0.020 0.001 TYR N 36 PHE 0.013 0.001 PHE J 78 TRP 0.019 0.001 TRP H 47 HIS 0.002 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21051) covalent geometry : angle 0.63115 / 0.30 (28617) SS BOND : bond 0.00424 / 0.24 ( 42) SS BOND : angle 1.03386 / 0.64 ( 84) hydrogen bonds : bond 0.03108 / 2.07 ( 621) hydrogen bonds : angle 5.16804 / 3.74 ( 1602) link_ALPHA1-3 : bond 0.00457 / 0.28 ( 9) link_ALPHA1-3 : angle 2.48267 / 1.71 ( 27) link_ALPHA1-6 : bond 0.00059 / 0.03 ( 6) link_ALPHA1-6 : angle 1.72856 / 0.96 ( 18) link_BETA1-4 : bond 0.00422 / 0.27 ( 42) link_BETA1-4 : angle 1.63034 / 1.14 ( 126) link_NAG-ASN : bond 0.00543 / 0.33 ( 66) link_NAG-ASN : angle 2.42351 / 1.68 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.95 seconds wall clock time: 58 minutes 19.82 seconds (3499.82 seconds total)