Starting phenix.real_space_refine on Fri Aug 7 10:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yht_72973/08_2026/9yht_72973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yht_72973/08_2026/9yht_72973.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9yht_72973/08_2026/9yht_72973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yht_72973/08_2026/9yht_72973.map" model { file = "/net/cci-nas-00/data/ceres_data/9yht_72973/08_2026/9yht_72973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yht_72973/08_2026/9yht_72973.cif" } 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= 0.000 sd= 0.009 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 12810 2.51 5 N 3426 2.21 5 O 4125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 20484 Number of models: 1 Model: "" Number of chains: 51 Chain: "C" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 974 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 974 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 974 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "N" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 1, '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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "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, 'GLC': 1, 'MAN': 1, '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: 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: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 1, '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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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 Time building chain proxies: 4.36, per 1000 atoms: 0.21 Number of scatterers: 20484 At special positions: 0 Unit cell: (159.21, 160.08, 131.37, 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 4125 8.00 N 3426 7.00 C 12810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 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=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.04 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=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 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 P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA l 3 " - " MAN l 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " GLC S 5 " " BMA a 3 " - " MAN a 5 " " BMA d 3 " - " GLC d 5 " " BMA l 3 " - " MAN l 5 " " BMA o 3 " - " GLC o 5 " 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 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 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 a 2 " - " BMA a 3 " " 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 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG D 1 " - " ASN G 156 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 230 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 344 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 197 " " NAG F 604 " - " ASN F 230 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 344 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 230 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 344 " " NAG I 1 " - " ASN G 160 " " NAG O 1 " - " ASN G 234 " " NAG P 1 " - " ASN G 262 " " NAG Q 1 " - " ASN G 276 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 332 " " NAG T 1 " - " ASN G 339 " " NAG U 1 " - " ASN G 386 " " NAG V 1 " - " ASN G 392 " " NAG W 1 " - " ASN G 448 " " NAG X 1 " - " ASN F 156 " " NAG Y 1 " - " ASN F 160 " " NAG Z 1 " - " ASN F 234 " " NAG a 1 " - " ASN F 262 " " NAG b 1 " - " ASN F 276 " " NAG c 1 " - " ASN F 295 " " NAG d 1 " - " ASN F 332 " " NAG e 1 " - " ASN F 339 " " NAG f 1 " - " ASN F 386 " " NAG g 1 " - " ASN F 392 " " NAG h 1 " - " ASN F 448 " " NAG i 1 " - " ASN E 156 " " NAG j 1 " - " ASN E 160 " " NAG k 1 " - " ASN E 234 " " NAG l 1 " - " ASN E 262 " " NAG m 1 " - " ASN E 276 " " NAG n 1 " - " ASN E 295 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 339 " " NAG q 1 " - " ASN E 386 " " NAG r 1 " - " ASN E 392 " " NAG s 1 " - " ASN E 448 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 831.6 milliseconds 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4482 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 21.5% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.434A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 544 removed outlier: 3.777A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.545A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 651 removed outlier: 3.715A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.780A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.423A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.510A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (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 195 through 198 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: 3.705A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.138A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.592A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.545A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.434A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.778A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.547A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.716A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.779A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.423A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.510A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (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 195 through 198 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: 3.705A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.533A 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: 4.138A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.591A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.545A pdb=" N VAL K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.434A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.777A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.546A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 removed outlier: 3.715A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.779A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.423A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.510A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (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 195 through 198 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: 3.705A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.533A 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: 4.138A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.591A pdb=" N LYS M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.544A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 604 through 609 removed outlier: 3.603A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.659A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.516A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.731A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 174 Processing sheet with id=AA6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.726A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.649A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 297 current: chain 'G' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.583A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 446 through 456 current: chain 'G' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'G' and resid 301 through 308 removed outlier: 3.806A pdb=" N THR G 303 " --> pdb=" O ASP G 321A" (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP G 321A" --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR H 100 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY G 324 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.514A pdb=" N ALA H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.914A pdb=" N SER H 58 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N TRP H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR H 90 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.498A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 604 through 609 removed outlier: 3.603A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.658A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.516A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.730A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AC3, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.726A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 260 through 261 removed outlier: 3.651A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 297 current: chain 'F' and resid 358 through 361 Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.583A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 446 through 456 current: chain 'F' and resid 413 through 416 Processing sheet with id=AC6, first strand: chain 'F' and resid 301 through 308 removed outlier: 3.807A pdb=" N THR F 303 " --> pdb=" O ASP F 321A" (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS F 305 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TYR J 100 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY F 324 " --> pdb=" O TYR J 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AC8, first strand: chain 'J' and resid 4 through 5 removed outlier: 3.514A pdb=" N ALA J 23 " --> pdb=" O GLN J 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AD1, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.914A pdb=" N SER J 58 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N TRP J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR J 90 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.498A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.606A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.658A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.515A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.731A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.726A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 260 through 261 removed outlier: 3.650A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 297 current: chain 'E' and resid 358 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.583A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 446 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AE3, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.806A pdb=" N THR E 303 " --> pdb=" O ASP E 321A" (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR M 100 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY E 324 " --> pdb=" O TYR M 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AE5, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.514A pdb=" N ALA M 23 " --> pdb=" O GLN M 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE M 78 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'M' and resid 58 through 59 removed outlier: 3.913A pdb=" N SER M 58 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N TRP M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE M 37 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR M 90 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.498A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1620 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: 4.23 Time building geometry restraints manager: 2.45 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: 6416 1.34 - 1.47: 5352 1.47 - 1.59: 8992 1.59 - 1.72: 0 1.72 - 1.84: 159 Bond restraints: 20919 Sorted by residual: bond pdb=" C4 NAG X 1 " pdb=" O4 NAG X 1 " ideal model delta sigma weight residual 1.409 1.444 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C4 NAG i 1 " pdb=" O4 NAG i 1 " ideal model delta sigma weight residual 1.409 1.444 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.443 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C2 BMA o 3 " pdb=" O2 BMA o 3 " ideal model delta sigma weight residual 1.402 1.436 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C2 BMA S 3 " pdb=" O2 BMA S 3 " ideal model delta sigma weight residual 1.402 1.434 -0.032 2.00e-02 2.50e+03 2.64e+00 ... (remaining 20914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 27440 1.63 - 3.27: 854 3.27 - 4.90: 104 4.90 - 6.53: 21 6.53 - 8.17: 24 Bond angle restraints: 28443 Sorted by residual: angle pdb=" C1 BMA a 3 " pdb=" O5 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 118.82 110.65 8.17 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C1 BMA P 3 " pdb=" O5 BMA P 3 " pdb=" C5 BMA P 3 " ideal model delta sigma weight residual 118.82 110.66 8.16 3.00e+00 1.11e-01 7.40e+00 angle pdb=" C1 BMA l 3 " pdb=" O5 BMA l 3 " pdb=" C5 BMA l 3 " ideal model delta sigma weight residual 118.82 110.68 8.14 3.00e+00 1.11e-01 7.37e+00 angle pdb=" C1 BMA o 3 " pdb=" O5 BMA o 3 " pdb=" C5 BMA o 3 " ideal model delta sigma weight residual 118.82 110.74 8.08 3.00e+00 1.11e-01 7.26e+00 angle pdb=" C1 BMA d 3 " pdb=" O5 BMA d 3 " pdb=" C5 BMA d 3 " ideal model delta sigma weight residual 118.82 110.76 8.06 3.00e+00 1.11e-01 7.21e+00 ... (remaining 28438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 12835 24.57 - 49.14: 840 49.14 - 73.71: 89 73.71 - 98.28: 39 98.28 - 122.85: 105 Dihedral angle restraints: 13908 sinusoidal: 6948 harmonic: 6960 Sorted by residual: dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.92 -63.92 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.92 -63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 13905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.024: 3459 1.024 - 2.048: 0 2.048 - 3.072: 0 3.072 - 4.096: 0 4.096 - 5.120: 21 Chirality restraints: 3480 Sorted by residual: chirality pdb=" C4 NAG F 602 " pdb=" C3 NAG F 602 " pdb=" C5 NAG F 602 " pdb=" O4 NAG F 602 " both_signs ideal model delta sigma weight residual False -2.53 2.59 -5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" C4 NAG E 602 " pdb=" C3 NAG E 602 " pdb=" C5 NAG E 602 " pdb=" O4 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.53 2.59 -5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" C4 NAG G 602 " pdb=" C3 NAG G 602 " pdb=" C5 NAG G 602 " pdb=" O4 NAG G 602 " both_signs ideal model delta sigma weight residual False -2.53 2.59 -5.12 2.00e-01 2.50e+01 6.55e+02 ... (remaining 3477 not shown) Planarity restraints: 3540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO E 43 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 42 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO F 43 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 43 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 42 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO G 43 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 43 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 43 " -0.023 5.00e-02 4.00e+02 ... (remaining 3537 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 10338 2.98 - 3.46: 19359 3.46 - 3.94: 32364 3.94 - 4.42: 35228 4.42 - 4.90: 58235 Nonbonded interactions: 155524 Sorted by model distance: nonbonded pdb=" C4 NAG k 1 " pdb=" O5 NAG k 2 " model vdw 2.496 2.776 nonbonded pdb=" C4 NAG O 1 " pdb=" O5 NAG O 2 " model vdw 2.497 2.776 nonbonded pdb=" C4 NAG Z 1 " pdb=" O5 NAG Z 2 " model vdw 2.497 2.776 nonbonded pdb=" O ILE B 635 " pdb=" CG2 ILE B 635 " model vdw 2.500 3.460 nonbonded pdb=" O ILE C 635 " pdb=" CG2 ILE C 635 " model vdw 2.500 3.460 ... (remaining 155519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } 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 'P' and resid 1 through 4) selection = (chain 'S' and resid 1 through 4) selection = (chain 'a' and resid 1 through 4) selection = (chain 'd' and resid 1 through 4) selection = (chain 'l' and resid 1 through 4) selection = (chain 'o' and resid 1 through 4) } 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.035 21072 Z= 0.232 Angle : 0.680 9.628 28857 Z= 0.284 Chirality : 0.391 5.120 3480 Planarity : 0.003 0.043 3483 Dihedral : 19.159 122.852 9291 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.99 % Allowed : 8.97 % Favored : 90.05 % 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: -0.56 (0.18), residues: 2370 helix: 2.18 (0.29), residues: 396 sheet: -0.29 (0.21), residues: 597 loop : -1.22 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 542 TYR 0.015 0.001 TYR J 33 PHE 0.009 0.001 PHE H 78 TRP 0.006 0.001 TRP E 112 HIS 0.002 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (20919) covalent geometry : angle 0.65031 / 0.28 (28443) SS BOND : bond 0.00548 / 0.38 ( 45) SS BOND : angle 1.11850 / 0.86 ( 90) hydrogen bonds : bond 0.14167 / 9.08 ( 624) hydrogen bonds : angle 6.17620 / 4.49 ( 1620) link_ALPHA1-3 : bond 0.00209 / 0.11 ( 6) link_ALPHA1-3 : angle 0.70095 / 0.37 ( 18) link_ALPHA1-6 : bond 0.00307 / 0.15 ( 6) link_ALPHA1-6 : angle 0.50910 / 0.30 ( 18) link_BETA1-4 : bond 0.00772 / 0.54 ( 39) link_BETA1-4 : angle 2.34412 / 1.64 ( 117) link_NAG-ASN : bond 0.00303 / 0.20 ( 57) link_NAG-ASN : angle 1.78434 / 1.23 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 580 time to evaluate : 0.749 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 530 MET cc_start: 0.8363 (tpp) cc_final: 0.7826 (tpp) REVERT: C 534 SER cc_start: 0.8741 (m) cc_final: 0.7911 (t) REVERT: C 538 THR cc_start: 0.8805 (p) cc_final: 0.8512 (p) REVERT: C 577 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 633 LYS cc_start: 0.8428 (tppt) cc_final: 0.8091 (tppt) REVERT: C 660 LEU cc_start: 0.8927 (tp) cc_final: 0.8708 (mm) REVERT: G 82 GLN cc_start: 0.7881 (mp10) cc_final: 0.7668 (mt0) REVERT: G 99 ASN cc_start: 0.8427 (t0) cc_final: 0.8018 (t0) REVERT: G 161 MET cc_start: 0.8457 (tpp) cc_final: 0.7593 (tpt) REVERT: G 180 ASP cc_start: 0.8951 (m-30) cc_final: 0.8697 (m-30) REVERT: G 300 ASN cc_start: 0.8586 (p0) cc_final: 0.8348 (p0) REVERT: H 50 ILE cc_start: 0.7225 (mm) cc_final: 0.6829 (mm) REVERT: H 77 GLN cc_start: 0.7519 (mm110) cc_final: 0.7319 (mm110) REVERT: H 91 TYR cc_start: 0.7340 (m-80) cc_final: 0.6685 (m-10) REVERT: B 534 SER cc_start: 0.8851 (m) cc_final: 0.8132 (p) REVERT: B 577 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 651 ASN cc_start: 0.6665 (m110) cc_final: 0.6265 (m110) REVERT: B 660 LEU cc_start: 0.8932 (tp) cc_final: 0.8536 (mp) REVERT: F 82 GLN cc_start: 0.7973 (mp10) cc_final: 0.7742 (mt0) REVERT: F 99 ASN cc_start: 0.8395 (t0) cc_final: 0.8101 (t0) REVERT: F 180 ASP cc_start: 0.8863 (m-30) cc_final: 0.8579 (m-30) REVERT: F 428 GLN cc_start: 0.8350 (mp10) cc_final: 0.8075 (mp10) REVERT: J 39 GLN cc_start: 0.6359 (tp40) cc_final: 0.5732 (tp40) REVERT: J 50 ILE cc_start: 0.7398 (mm) cc_final: 0.6997 (mm) REVERT: J 51 ILE cc_start: 0.8791 (tp) cc_final: 0.8590 (tp) REVERT: J 52 SER cc_start: 0.6574 (p) cc_final: 0.6303 (m) REVERT: J 75 LYS cc_start: 0.8569 (pttt) cc_final: 0.8271 (ptpp) REVERT: J 89 VAL cc_start: 0.8053 (m) cc_final: 0.7638 (m) REVERT: J 91 TYR cc_start: 0.7511 (m-80) cc_final: 0.6907 (m-10) REVERT: K 36 TYR cc_start: 0.8307 (m-80) cc_final: 0.8038 (m-80) REVERT: A 530 MET cc_start: 0.8475 (tpp) cc_final: 0.8149 (tpp) REVERT: A 534 SER cc_start: 0.8820 (m) cc_final: 0.8574 (p) REVERT: A 660 LEU cc_start: 0.8789 (tp) cc_final: 0.8534 (mp) REVERT: E 82 GLN cc_start: 0.7948 (mp10) cc_final: 0.7604 (mt0) REVERT: E 99 ASN cc_start: 0.8326 (t0) cc_final: 0.7802 (t0) REVERT: E 161 MET cc_start: 0.8248 (tpp) cc_final: 0.7607 (tpt) REVERT: E 180 ASP cc_start: 0.8802 (m-30) cc_final: 0.8488 (m-30) REVERT: E 213 ILE cc_start: 0.8923 (pt) cc_final: 0.8699 (pt) REVERT: E 308 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8706 (mmt90) REVERT: M 50 ILE cc_start: 0.6927 (mm) cc_final: 0.6680 (mm) REVERT: M 75 LYS cc_start: 0.8435 (pttt) cc_final: 0.8129 (ttpt) REVERT: M 89 VAL cc_start: 0.7743 (m) cc_final: 0.7488 (m) REVERT: M 91 TYR cc_start: 0.7358 (m-80) cc_final: 0.6892 (m-10) REVERT: N 36 TYR cc_start: 0.8321 (m-80) cc_final: 0.7568 (m-80) REVERT: N 74 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7497 (ttpp) outliers start: 21 outliers final: 9 residues processed: 600 average time/residue: 0.1396 time to fit residues: 131.1533 Evaluate side-chains 378 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 369 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 8.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 590 GLN G 85 HIS G 203 GLN G 440 GLN B 590 GLN B 652 GLN F 85 HIS F 203 GLN F 440 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A 590 GLN A 591 GLN A 652 GLN E 85 HIS E 203 GLN E 330 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090816 restraints weight = 39406.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092350 restraints weight = 29046.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093390 restraints weight = 24068.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094057 restraints weight = 19855.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094370 restraints weight = 19062.323| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21072 Z= 0.175 Angle : 0.763 11.106 28857 Z= 0.341 Chirality : 0.051 0.429 3480 Planarity : 0.004 0.058 3483 Dihedral : 10.742 83.768 4827 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % 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 (0.18), residues: 2370 helix: 1.70 (0.27), residues: 411 sheet: -0.37 (0.21), residues: 615 loop : -1.27 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 429 TYR 0.015 0.001 TYR J 33 PHE 0.022 0.002 PHE H 78 TRP 0.013 0.001 TRP M 36 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (20919) covalent geometry : angle 0.70320 / 0.33 (28443) SS BOND : bond 0.00617 / 0.38 ( 45) SS BOND : angle 2.20674 / 1.57 ( 90) hydrogen bonds : bond 0.03337 / 2.22 ( 624) hydrogen bonds : angle 5.18534 / 3.71 ( 1620) link_ALPHA1-3 : bond 0.00773 / 0.41 ( 6) link_ALPHA1-3 : angle 2.76647 / 1.60 ( 18) link_ALPHA1-6 : bond 0.00564 / 0.29 ( 6) link_ALPHA1-6 : angle 1.50982 / 0.89 ( 18) link_BETA1-4 : bond 0.00815 / 0.59 ( 39) link_BETA1-4 : angle 2.63958 / 1.83 ( 117) link_NAG-ASN : bond 0.00517 / 0.34 ( 57) link_NAG-ASN : angle 2.75203 / 1.96 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 429 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 530 MET cc_start: 0.8491 (tpp) cc_final: 0.8245 (tpp) REVERT: C 534 SER cc_start: 0.8888 (m) cc_final: 0.8190 (t) REVERT: C 577 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 591 GLN cc_start: 0.8810 (tt0) cc_final: 0.8499 (tt0) REVERT: C 626 MET cc_start: 0.9097 (ttm) cc_final: 0.8285 (ttm) REVERT: C 633 LYS cc_start: 0.8354 (tppt) cc_final: 0.8093 (tppt) REVERT: G 99 ASN cc_start: 0.8469 (t0) cc_final: 0.8004 (t0) REVERT: G 161 MET cc_start: 0.8476 (tpp) cc_final: 0.7727 (tpt) REVERT: G 274 SER cc_start: 0.8941 (t) cc_final: 0.8690 (t) REVERT: G 475 MET cc_start: 0.8930 (mmm) cc_final: 0.8672 (mmm) REVERT: H 30 ARG cc_start: 0.8365 (mtt90) cc_final: 0.8051 (mtm-85) REVERT: H 45 LEU cc_start: 0.4137 (pp) cc_final: 0.3772 (pp) REVERT: H 91 TYR cc_start: 0.8037 (m-80) cc_final: 0.7662 (m-10) REVERT: L 50 LYS cc_start: 0.6842 (mttt) cc_final: 0.5541 (tmtt) REVERT: B 534 SER cc_start: 0.9031 (m) cc_final: 0.8351 (p) REVERT: B 630 GLN cc_start: 0.8910 (pm20) cc_final: 0.8683 (pm20) REVERT: B 651 ASN cc_start: 0.6726 (m110) cc_final: 0.6501 (m110) REVERT: B 660 LEU cc_start: 0.8971 (tp) cc_final: 0.8639 (mp) REVERT: F 99 ASN cc_start: 0.8496 (t0) cc_final: 0.8139 (t0) REVERT: F 180 ASP cc_start: 0.8889 (m-30) cc_final: 0.8670 (m-30) REVERT: F 428 GLN cc_start: 0.8526 (mp10) cc_final: 0.8172 (mp10) REVERT: J 30 ARG cc_start: 0.8310 (mtt90) cc_final: 0.8029 (mtm-85) REVERT: A 538 THR cc_start: 0.8851 (p) cc_final: 0.8586 (p) REVERT: A 651 ASN cc_start: 0.6812 (m110) cc_final: 0.6542 (m110) REVERT: E 49 GLU cc_start: 0.7925 (pm20) cc_final: 0.7674 (pm20) REVERT: E 82 GLN cc_start: 0.7976 (mp10) cc_final: 0.7748 (mt0) REVERT: E 99 ASN cc_start: 0.8443 (t0) cc_final: 0.7893 (t0) REVERT: E 161 MET cc_start: 0.8357 (tpp) cc_final: 0.7607 (tpt) REVERT: E 180 ASP cc_start: 0.8832 (m-30) cc_final: 0.8505 (m-30) REVERT: M 39 GLN cc_start: 0.6167 (tp40) cc_final: 0.5962 (tp-100) REVERT: M 50 ILE cc_start: 0.7609 (mm) cc_final: 0.6973 (mm) REVERT: N 36 TYR cc_start: 0.8531 (m-80) cc_final: 0.7879 (m-80) REVERT: N 74 LYS cc_start: 0.8660 (mtmt) cc_final: 0.7815 (ttpp) outliers start: 3 outliers final: 2 residues processed: 432 average time/residue: 0.1264 time to fit residues: 87.6389 Evaluate side-chains 334 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 228 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 164 optimal weight: 0.0470 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 82 GLN G 203 GLN H 39 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN F 203 GLN F 330 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN E 203 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.089088 restraints weight = 39495.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091195 restraints weight = 27939.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091997 restraints weight = 22410.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.092924 restraints weight = 18588.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093248 restraints weight = 17021.725| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21072 Z= 0.153 Angle : 0.688 10.821 28857 Z= 0.318 Chirality : 0.050 0.365 3480 Planarity : 0.004 0.056 3483 Dihedral : 10.346 119.702 4827 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2370 helix: 1.58 (0.28), residues: 411 sheet: -0.45 (0.20), residues: 627 loop : -1.26 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 100I TYR 0.020 0.001 TYR J 33 PHE 0.037 0.002 PHE N 62 TRP 0.022 0.001 TRP J 36 HIS 0.008 0.001 HIS K 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (20919) covalent geometry : angle 0.63682 / 0.30 (28443) SS BOND : bond 0.00517 / 0.35 ( 45) SS BOND : angle 1.90047 / 1.39 ( 90) hydrogen bonds : bond 0.03311 / 2.20 ( 624) hydrogen bonds : angle 5.19408 / 3.66 ( 1620) link_ALPHA1-3 : bond 0.01091 / 0.59 ( 6) link_ALPHA1-3 : angle 2.12120 / 1.21 ( 18) link_ALPHA1-6 : bond 0.00809 / 0.41 ( 6) link_ALPHA1-6 : angle 1.55630 / 0.88 ( 18) link_BETA1-4 : bond 0.00837 / 0.58 ( 39) link_BETA1-4 : angle 2.47252 / 1.71 ( 117) link_NAG-ASN : bond 0.00345 / 0.24 ( 57) link_NAG-ASN : angle 2.39211 / 1.63 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.751 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: C 534 SER cc_start: 0.8895 (m) cc_final: 0.8324 (t) REVERT: C 626 MET cc_start: 0.9223 (ttm) cc_final: 0.8799 (ttt) REVERT: C 630 GLN cc_start: 0.8852 (pm20) cc_final: 0.8629 (pm20) REVERT: C 633 LYS cc_start: 0.8377 (tppt) cc_final: 0.8098 (tppt) REVERT: C 651 ASN cc_start: 0.7229 (m110) cc_final: 0.6611 (m110) REVERT: G 99 ASN cc_start: 0.8500 (t0) cc_final: 0.7973 (t0) REVERT: G 161 MET cc_start: 0.8423 (tpp) cc_final: 0.7736 (tpt) REVERT: G 180 ASP cc_start: 0.9028 (m-30) cc_final: 0.8808 (m-30) REVERT: H 30 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7848 (ttm170) REVERT: L 50 LYS cc_start: 0.6817 (mttt) cc_final: 0.5374 (tmtt) REVERT: L 59 PRO cc_start: 0.7051 (Cg_endo) cc_final: 0.6811 (Cg_exo) REVERT: B 534 SER cc_start: 0.9006 (m) cc_final: 0.8338 (p) REVERT: B 538 THR cc_start: 0.8973 (p) cc_final: 0.8517 (t) REVERT: B 626 MET cc_start: 0.9150 (ttm) cc_final: 0.8917 (ttt) REVERT: B 660 LEU cc_start: 0.9026 (tp) cc_final: 0.8646 (mp) REVERT: F 99 ASN cc_start: 0.8538 (t0) cc_final: 0.8066 (t0) REVERT: F 274 SER cc_start: 0.9024 (t) cc_final: 0.8822 (t) REVERT: F 428 GLN cc_start: 0.8559 (mp10) cc_final: 0.8148 (mp10) REVERT: J 5 GLN cc_start: 0.5577 (mp10) cc_final: 0.5062 (tt0) REVERT: J 30 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7912 (mtm-85) REVERT: J 39 GLN cc_start: 0.6571 (tp-100) cc_final: 0.6119 (tp40) REVERT: J 51 ILE cc_start: 0.8664 (tp) cc_final: 0.8462 (tp) REVERT: J 75 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7924 (ttpt) REVERT: A 650 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6438 (tm-30) REVERT: A 653 GLN cc_start: 0.7702 (mt0) cc_final: 0.7303 (mm-40) REVERT: E 99 ASN cc_start: 0.8512 (t0) cc_final: 0.7770 (t0) REVERT: E 142 MET cc_start: 0.8837 (tpp) cc_final: 0.8401 (tpt) REVERT: E 161 MET cc_start: 0.8318 (tpp) cc_final: 0.7698 (tpt) REVERT: E 180 ASP cc_start: 0.8880 (m-30) cc_final: 0.8586 (m-30) REVERT: M 36 TRP cc_start: 0.7745 (m100) cc_final: 0.7445 (m100) REVERT: M 91 TYR cc_start: 0.7945 (m-10) cc_final: 0.7551 (m-10) REVERT: N 104 VAL cc_start: 0.2974 (m) cc_final: 0.2717 (p) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.1290 time to fit residues: 84.1411 Evaluate side-chains 322 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 348 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN A 591 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** M 6 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 = 0.3466 r_free = 0.3466 target = 0.117485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.086818 restraints weight = 39992.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.088681 restraints weight = 30002.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089476 restraints weight = 23253.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090188 restraints weight = 20431.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.090390 restraints weight = 19297.541| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21072 Z= 0.200 Angle : 0.735 10.969 28857 Z= 0.338 Chirality : 0.051 0.335 3480 Planarity : 0.004 0.054 3483 Dihedral : 9.964 120.561 4827 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 0.14 % Allowed : 4.08 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.17), residues: 2370 helix: 1.31 (0.27), residues: 411 sheet: -0.55 (0.20), residues: 609 loop : -1.30 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.021 0.002 TYR G 217 PHE 0.021 0.002 PHE H 78 TRP 0.021 0.002 TRP G 45 HIS 0.005 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (20919) covalent geometry : angle 0.67516 / 0.32 (28443) SS BOND : bond 0.00539 / 0.36 ( 45) SS BOND : angle 1.97993 / 1.49 ( 90) hydrogen bonds : bond 0.03329 / 2.23 ( 624) hydrogen bonds : angle 5.20211 / 3.67 ( 1620) link_ALPHA1-3 : bond 0.01082 / 0.59 ( 6) link_ALPHA1-3 : angle 2.45391 / 1.42 ( 18) link_ALPHA1-6 : bond 0.00908 / 0.46 ( 6) link_ALPHA1-6 : angle 1.72519 / 0.95 ( 18) link_BETA1-4 : bond 0.00773 / 0.54 ( 39) link_BETA1-4 : angle 2.56644 / 1.77 ( 117) link_NAG-ASN : bond 0.00388 / 0.26 ( 57) link_NAG-ASN : angle 2.79191 / 1.97 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 403 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8903 (m) cc_final: 0.8382 (t) REVERT: C 591 GLN cc_start: 0.8828 (tt0) cc_final: 0.8430 (tt0) REVERT: C 630 GLN cc_start: 0.8797 (pm20) cc_final: 0.8493 (pm20) REVERT: C 633 LYS cc_start: 0.8431 (tppt) cc_final: 0.8222 (tppt) REVERT: G 99 ASN cc_start: 0.8559 (t0) cc_final: 0.7950 (t0) REVERT: G 142 MET cc_start: 0.8902 (tpp) cc_final: 0.8656 (tpt) REVERT: G 161 MET cc_start: 0.8535 (tpp) cc_final: 0.7875 (tpt) REVERT: G 180 ASP cc_start: 0.9028 (m-30) cc_final: 0.8629 (m-30) REVERT: G 274 SER cc_start: 0.8879 (t) cc_final: 0.8659 (t) REVERT: H 30 ARG cc_start: 0.8456 (mtt90) cc_final: 0.8008 (mtm-85) REVERT: H 39 GLN cc_start: 0.6106 (tp40) cc_final: 0.5375 (tp40) REVERT: H 89 VAL cc_start: 0.7713 (m) cc_final: 0.7197 (p) REVERT: L 50 LYS cc_start: 0.6996 (mttt) cc_final: 0.5531 (tmtt) REVERT: B 534 SER cc_start: 0.9038 (m) cc_final: 0.8287 (p) REVERT: B 538 THR cc_start: 0.9002 (p) cc_final: 0.8528 (t) REVERT: B 626 MET cc_start: 0.9111 (ttm) cc_final: 0.8830 (ttt) REVERT: B 627 THR cc_start: 0.9339 (p) cc_final: 0.8919 (p) REVERT: B 630 GLN cc_start: 0.8908 (pm20) cc_final: 0.8380 (pm20) REVERT: B 640 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8127 (mm-40) REVERT: F 142 MET cc_start: 0.8812 (tpp) cc_final: 0.8395 (tpt) REVERT: J 30 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7734 (ttm110) REVERT: J 39 GLN cc_start: 0.6374 (tp40) cc_final: 0.5934 (tp-100) REVERT: J 50 ILE cc_start: 0.7888 (mm) cc_final: 0.7173 (mm) REVERT: J 51 ILE cc_start: 0.8668 (tp) cc_final: 0.8434 (tp) REVERT: J 75 LYS cc_start: 0.8343 (ptpp) cc_final: 0.7872 (ttpt) REVERT: J 86 ASP cc_start: 0.6527 (m-30) cc_final: 0.6274 (m-30) REVERT: K 49 TYR cc_start: 0.6045 (p90) cc_final: 0.5737 (p90) REVERT: A 577 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 626 MET cc_start: 0.8875 (ttm) cc_final: 0.8502 (ttm) REVERT: A 630 GLN cc_start: 0.8849 (pm20) cc_final: 0.8630 (pm20) REVERT: A 653 GLN cc_start: 0.7740 (mt0) cc_final: 0.7367 (mm-40) REVERT: E 99 ASN cc_start: 0.8648 (t0) cc_final: 0.7901 (t0) REVERT: E 142 MET cc_start: 0.8810 (tpp) cc_final: 0.8446 (tpt) REVERT: E 161 MET cc_start: 0.8417 (tpp) cc_final: 0.7821 (tpt) REVERT: E 180 ASP cc_start: 0.9001 (m-30) cc_final: 0.8738 (m-30) REVERT: M 36 TRP cc_start: 0.7796 (m100) cc_final: 0.7227 (m100) REVERT: M 75 LYS cc_start: 0.8566 (ptpp) cc_final: 0.8283 (ttpt) REVERT: N 104 VAL cc_start: 0.3372 (m) cc_final: 0.3160 (p) outliers start: 3 outliers final: 0 residues processed: 405 average time/residue: 0.1226 time to fit residues: 79.5432 Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 78 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 142 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 591 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS G 348 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 590 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088536 restraints weight = 39388.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.090480 restraints weight = 29777.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091210 restraints weight = 23363.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091642 restraints weight = 20432.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091985 restraints weight = 19584.342| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21072 Z= 0.136 Angle : 0.684 9.856 28857 Z= 0.315 Chirality : 0.050 0.333 3480 Planarity : 0.004 0.055 3483 Dihedral : 9.466 119.326 4827 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer: Outliers : 0.14 % Allowed : 2.63 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2370 helix: 1.29 (0.27), residues: 411 sheet: -0.56 (0.20), residues: 627 loop : -1.26 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 100I TYR 0.021 0.001 TYR J 33 PHE 0.016 0.001 PHE H 78 TRP 0.028 0.001 TRP J 36 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (20919) covalent geometry : angle 0.63326 / 0.30 (28443) SS BOND : bond 0.00425 / 0.28 ( 45) SS BOND : angle 1.62681 / 1.22 ( 90) hydrogen bonds : bond 0.03068 / 2.04 ( 624) hydrogen bonds : angle 5.10461 / 3.60 ( 1620) link_ALPHA1-3 : bond 0.01204 / 0.65 ( 6) link_ALPHA1-3 : angle 2.30694 / 1.34 ( 18) link_ALPHA1-6 : bond 0.01078 / 0.55 ( 6) link_ALPHA1-6 : angle 1.64014 / 0.90 ( 18) link_BETA1-4 : bond 0.00796 / 0.56 ( 39) link_BETA1-4 : angle 2.48619 / 1.72 ( 117) link_NAG-ASN : bond 0.00295 / 0.20 ( 57) link_NAG-ASN : angle 2.41493 / 1.66 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 403 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8863 (m) cc_final: 0.8387 (t) REVERT: C 630 GLN cc_start: 0.8748 (pm20) cc_final: 0.8526 (pm20) REVERT: C 633 LYS cc_start: 0.8499 (tppt) cc_final: 0.8245 (tppt) REVERT: G 67 ASN cc_start: 0.9084 (t0) cc_final: 0.8799 (t0) REVERT: G 99 ASN cc_start: 0.8560 (t0) cc_final: 0.7923 (t0) REVERT: G 142 MET cc_start: 0.8837 (tpp) cc_final: 0.8288 (tpt) REVERT: G 161 MET cc_start: 0.8510 (tpp) cc_final: 0.7899 (tpt) REVERT: G 180 ASP cc_start: 0.9012 (m-30) cc_final: 0.8633 (m-30) REVERT: G 274 SER cc_start: 0.9019 (t) cc_final: 0.8773 (t) REVERT: H 30 ARG cc_start: 0.8422 (mtt90) cc_final: 0.7987 (mtm-85) REVERT: H 36 TRP cc_start: 0.7758 (m100) cc_final: 0.7226 (m100) REVERT: H 37 ILE cc_start: 0.8873 (tt) cc_final: 0.8573 (tt) REVERT: H 89 VAL cc_start: 0.7775 (m) cc_final: 0.7231 (p) REVERT: H 91 TYR cc_start: 0.8292 (m-10) cc_final: 0.7649 (m-10) REVERT: L 50 LYS cc_start: 0.7062 (mttt) cc_final: 0.5653 (tmtt) REVERT: B 534 SER cc_start: 0.8971 (m) cc_final: 0.8299 (p) REVERT: B 538 THR cc_start: 0.8963 (p) cc_final: 0.8538 (t) REVERT: B 660 LEU cc_start: 0.9015 (tp) cc_final: 0.8670 (mp) REVERT: F 142 MET cc_start: 0.8704 (tpp) cc_final: 0.8337 (tpt) REVERT: J 30 ARG cc_start: 0.8325 (mtt90) cc_final: 0.7710 (ttm110) REVERT: J 39 GLN cc_start: 0.6382 (tp40) cc_final: 0.5909 (tp40) REVERT: J 75 LYS cc_start: 0.8325 (ptpp) cc_final: 0.8087 (ptmm) REVERT: J 89 VAL cc_start: 0.8256 (m) cc_final: 0.7775 (p) REVERT: K 49 TYR cc_start: 0.5951 (p90) cc_final: 0.5679 (p90) REVERT: K 61 ARG cc_start: 0.7182 (ptt180) cc_final: 0.6917 (ptt180) REVERT: E 67 ASN cc_start: 0.9034 (t0) cc_final: 0.8770 (t0) REVERT: E 99 ASN cc_start: 0.8582 (t0) cc_final: 0.7767 (t0) REVERT: E 142 MET cc_start: 0.8765 (tpp) cc_final: 0.8457 (tpt) REVERT: E 161 MET cc_start: 0.8404 (tpp) cc_final: 0.7796 (tpt) REVERT: E 180 ASP cc_start: 0.9047 (m-30) cc_final: 0.8581 (m-30) REVERT: E 475 MET cc_start: 0.8777 (mmm) cc_final: 0.8417 (mmm) REVERT: M 36 TRP cc_start: 0.7846 (m100) cc_final: 0.7328 (m100) outliers start: 3 outliers final: 0 residues processed: 405 average time/residue: 0.1258 time to fit residues: 79.8537 Evaluate side-chains 314 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 211 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 200 optimal weight: 0.0040 chunk 147 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 121 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** M 39 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 = 0.3520 r_free = 0.3520 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.090018 restraints weight = 39171.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092610 restraints weight = 26974.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093320 restraints weight = 21030.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094473 restraints weight = 17106.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094745 restraints weight = 15415.513| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21072 Z= 0.116 Angle : 0.659 9.549 28857 Z= 0.304 Chirality : 0.049 0.309 3480 Planarity : 0.004 0.057 3483 Dihedral : 8.940 117.417 4827 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.98 (0.17), residues: 2370 helix: 1.15 (0.27), residues: 417 sheet: -0.51 (0.20), residues: 630 loop : -1.34 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 327 TYR 0.025 0.001 TYR G 217 PHE 0.016 0.001 PHE J 78 TRP 0.020 0.001 TRP N 96 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (20919) covalent geometry : angle 0.61573 / 0.29 (28443) SS BOND : bond 0.00371 / 0.25 ( 45) SS BOND : angle 1.45392 / 1.07 ( 90) hydrogen bonds : bond 0.03013 / 2.02 ( 624) hydrogen bonds : angle 5.07319 / 3.57 ( 1620) link_ALPHA1-3 : bond 0.01310 / 0.70 ( 6) link_ALPHA1-3 : angle 2.24681 / 1.31 ( 18) link_ALPHA1-6 : bond 0.01137 / 0.59 ( 6) link_ALPHA1-6 : angle 1.63594 / 0.88 ( 18) link_BETA1-4 : bond 0.00773 / 0.52 ( 39) link_BETA1-4 : angle 2.42392 / 1.66 ( 117) link_NAG-ASN : bond 0.00313 / 0.21 ( 57) link_NAG-ASN : angle 2.04553 / 1.41 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8825 (m) cc_final: 0.8441 (t) REVERT: C 630 GLN cc_start: 0.8678 (pm20) cc_final: 0.8410 (pm20) REVERT: C 633 LYS cc_start: 0.8508 (tppt) cc_final: 0.8186 (tppt) REVERT: G 67 ASN cc_start: 0.9014 (t0) cc_final: 0.8811 (t0) REVERT: G 142 MET cc_start: 0.8774 (tpp) cc_final: 0.8324 (tpt) REVERT: G 161 MET cc_start: 0.8533 (tpp) cc_final: 0.7818 (tpt) REVERT: G 180 ASP cc_start: 0.9026 (m-30) cc_final: 0.8676 (m-30) REVERT: H 30 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7451 (mtm-85) REVERT: H 36 TRP cc_start: 0.7785 (m100) cc_final: 0.7314 (m100) REVERT: H 39 GLN cc_start: 0.6414 (tp40) cc_final: 0.5874 (tp40) REVERT: H 89 VAL cc_start: 0.7826 (m) cc_final: 0.7344 (p) REVERT: H 91 TYR cc_start: 0.8266 (m-10) cc_final: 0.7583 (m-10) REVERT: L 50 LYS cc_start: 0.6790 (mttt) cc_final: 0.5499 (tmtt) REVERT: B 534 SER cc_start: 0.8893 (m) cc_final: 0.8412 (t) REVERT: B 538 THR cc_start: 0.8922 (p) cc_final: 0.8547 (t) REVERT: B 640 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8093 (mm-40) REVERT: B 660 LEU cc_start: 0.8983 (tp) cc_final: 0.8643 (mp) REVERT: F 99 ASN cc_start: 0.8480 (t0) cc_final: 0.7851 (t0) REVERT: F 142 MET cc_start: 0.8663 (tpp) cc_final: 0.8369 (tpt) REVERT: F 347 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8131 (tppt) REVERT: J 30 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7858 (mtm-85) REVERT: J 39 GLN cc_start: 0.6430 (tp40) cc_final: 0.5912 (tp40) REVERT: J 89 VAL cc_start: 0.8235 (m) cc_final: 0.7742 (p) REVERT: E 67 ASN cc_start: 0.8944 (t0) cc_final: 0.8738 (t0) REVERT: E 99 ASN cc_start: 0.8398 (t0) cc_final: 0.7590 (t0) REVERT: E 161 MET cc_start: 0.8408 (tpp) cc_final: 0.7617 (tpt) REVERT: E 180 ASP cc_start: 0.9025 (m-30) cc_final: 0.8640 (m-30) REVERT: M 30 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8067 (ttm170) REVERT: M 36 TRP cc_start: 0.7902 (m100) cc_final: 0.7494 (m100) REVERT: M 50 ILE cc_start: 0.7411 (mm) cc_final: 0.7129 (mm) REVERT: N 61 ARG cc_start: 0.7448 (ptt180) cc_final: 0.7174 (ptt180) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1146 time to fit residues: 72.9907 Evaluate side-chains 318 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 102 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 210 optimal weight: 0.0870 chunk 214 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN E 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089120 restraints weight = 39250.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091244 restraints weight = 27067.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092675 restraints weight = 20968.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093439 restraints weight = 17665.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094280 restraints weight = 15863.138| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21072 Z= 0.123 Angle : 0.653 9.553 28857 Z= 0.301 Chirality : 0.048 0.298 3480 Planarity : 0.004 0.056 3483 Dihedral : 8.672 117.313 4827 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 0.05 % Allowed : 1.31 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.91 (0.17), residues: 2370 helix: 1.51 (0.27), residues: 399 sheet: -0.48 (0.21), residues: 600 loop : -1.35 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 178 TYR 0.024 0.001 TYR F 217 PHE 0.015 0.001 PHE H 78 TRP 0.031 0.001 TRP J 36 HIS 0.007 0.001 HIS K 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (20919) covalent geometry : angle 0.61146 / 0.29 (28443) SS BOND : bond 0.00392 / 0.26 ( 45) SS BOND : angle 1.47820 / 1.11 ( 90) hydrogen bonds : bond 0.02987 / 2.00 ( 624) hydrogen bonds : angle 5.01570 / 3.51 ( 1620) link_ALPHA1-3 : bond 0.01271 / 0.68 ( 6) link_ALPHA1-3 : angle 2.26208 / 1.30 ( 18) link_ALPHA1-6 : bond 0.01218 / 0.63 ( 6) link_ALPHA1-6 : angle 1.72810 / 0.94 ( 18) link_BETA1-4 : bond 0.00766 / 0.53 ( 39) link_BETA1-4 : angle 2.39929 / 1.65 ( 117) link_NAG-ASN : bond 0.00305 / 0.21 ( 57) link_NAG-ASN : angle 1.94469 / 1.35 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8825 (m) cc_final: 0.8438 (t) REVERT: C 633 LYS cc_start: 0.8469 (tppt) cc_final: 0.8214 (tppt) REVERT: G 100 MET cc_start: 0.9222 (mtp) cc_final: 0.8975 (mtp) REVERT: G 142 MET cc_start: 0.8720 (tpp) cc_final: 0.8319 (tpt) REVERT: G 161 MET cc_start: 0.8553 (tpp) cc_final: 0.7818 (tpt) REVERT: G 180 ASP cc_start: 0.9020 (m-30) cc_final: 0.8665 (m-30) REVERT: G 274 SER cc_start: 0.8927 (t) cc_final: 0.8679 (t) REVERT: H 30 ARG cc_start: 0.8401 (mtt90) cc_final: 0.7479 (mtm-85) REVERT: H 36 TRP cc_start: 0.7752 (m100) cc_final: 0.7249 (m100) REVERT: H 89 VAL cc_start: 0.7833 (m) cc_final: 0.7388 (p) REVERT: H 91 TYR cc_start: 0.8251 (m-10) cc_final: 0.7641 (m-10) REVERT: L 50 LYS cc_start: 0.6938 (mttt) cc_final: 0.5559 (tmtt) REVERT: B 534 SER cc_start: 0.8917 (m) cc_final: 0.8426 (t) REVERT: B 538 THR cc_start: 0.8965 (p) cc_final: 0.8541 (t) REVERT: B 660 LEU cc_start: 0.8977 (tp) cc_final: 0.8646 (mp) REVERT: F 99 ASN cc_start: 0.8566 (t0) cc_final: 0.7926 (t0) REVERT: F 142 MET cc_start: 0.8653 (tpp) cc_final: 0.8411 (tpt) REVERT: F 217 TYR cc_start: 0.7676 (m-80) cc_final: 0.7462 (m-80) REVERT: F 300 ASN cc_start: 0.8659 (p0) cc_final: 0.8398 (p0) REVERT: F 347 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8151 (tppt) REVERT: J 30 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7869 (mtm-85) REVERT: J 39 GLN cc_start: 0.6443 (tp40) cc_final: 0.5938 (tp40) REVERT: J 50 ILE cc_start: 0.7990 (mm) cc_final: 0.7415 (mm) REVERT: J 51 ILE cc_start: 0.8322 (tp) cc_final: 0.7923 (tp) REVERT: J 75 LYS cc_start: 0.8489 (ptmt) cc_final: 0.8000 (ttpt) REVERT: J 89 VAL cc_start: 0.8210 (m) cc_final: 0.7709 (p) REVERT: A 577 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 99 ASN cc_start: 0.8388 (t0) cc_final: 0.7606 (t0) REVERT: E 161 MET cc_start: 0.8427 (tpp) cc_final: 0.7811 (tpt) REVERT: E 180 ASP cc_start: 0.9037 (m-30) cc_final: 0.8594 (m-30) REVERT: E 274 SER cc_start: 0.9105 (t) cc_final: 0.8880 (t) REVERT: E 475 MET cc_start: 0.8728 (mmm) cc_final: 0.8390 (mmm) REVERT: M 30 ARG cc_start: 0.8451 (mtt90) cc_final: 0.7995 (ttm170) REVERT: M 36 TRP cc_start: 0.7918 (m100) cc_final: 0.7596 (m100) REVERT: M 50 ILE cc_start: 0.7696 (mm) cc_final: 0.7143 (mm) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.1271 time to fit residues: 79.2004 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 : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 220 optimal weight: 20.0000 chunk 69 optimal weight: 0.0010 chunk 83 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090883 restraints weight = 39276.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092946 restraints weight = 27815.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093621 restraints weight = 22754.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094696 restraints weight = 18963.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094955 restraints weight = 17186.476| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21072 Z= 0.118 Angle : 0.661 9.547 28857 Z= 0.306 Chirality : 0.048 0.284 3480 Planarity : 0.004 0.057 3483 Dihedral : 8.454 116.448 4827 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2370 helix: 1.56 (0.28), residues: 399 sheet: -0.45 (0.21), residues: 594 loop : -1.35 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 61 TYR 0.019 0.001 TYR F 217 PHE 0.016 0.001 PHE N 98 TRP 0.018 0.001 TRP K 96 HIS 0.007 0.001 HIS N 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (20919) covalent geometry : angle 0.62226 / 0.30 (28443) SS BOND : bond 0.00373 / 0.25 ( 45) SS BOND : angle 1.47070 / 1.06 ( 90) hydrogen bonds : bond 0.02922 / 1.96 ( 624) hydrogen bonds : angle 4.95926 / 3.48 ( 1620) link_ALPHA1-3 : bond 0.01293 / 0.69 ( 6) link_ALPHA1-3 : angle 2.20446 / 1.29 ( 18) link_ALPHA1-6 : bond 0.01237 / 0.64 ( 6) link_ALPHA1-6 : angle 1.74821 / 0.95 ( 18) link_BETA1-4 : bond 0.00753 / 0.52 ( 39) link_BETA1-4 : angle 2.36964 / 1.63 ( 117) link_NAG-ASN : bond 0.00297 / 0.20 ( 57) link_NAG-ASN : angle 1.84487 / 1.29 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8835 (m) cc_final: 0.8454 (t) REVERT: C 633 LYS cc_start: 0.8479 (tppt) cc_final: 0.8179 (tppt) REVERT: C 651 ASN cc_start: 0.7192 (m110) cc_final: 0.6927 (m-40) REVERT: G 67 ASN cc_start: 0.8975 (t0) cc_final: 0.8773 (t0) REVERT: G 161 MET cc_start: 0.8552 (tpp) cc_final: 0.7837 (tpt) REVERT: G 180 ASP cc_start: 0.9015 (m-30) cc_final: 0.8679 (m-30) REVERT: G 274 SER cc_start: 0.8990 (t) cc_final: 0.8727 (t) REVERT: H 30 ARG cc_start: 0.8383 (mtt90) cc_final: 0.7451 (mtm-85) REVERT: H 36 TRP cc_start: 0.7855 (m100) cc_final: 0.7257 (m100) REVERT: H 89 VAL cc_start: 0.7713 (m) cc_final: 0.7297 (p) REVERT: H 91 TYR cc_start: 0.8272 (m-10) cc_final: 0.7652 (m-10) REVERT: L 50 LYS cc_start: 0.6719 (mttt) cc_final: 0.5490 (tmtt) REVERT: B 534 SER cc_start: 0.8920 (m) cc_final: 0.8454 (t) REVERT: B 538 THR cc_start: 0.8859 (p) cc_final: 0.8476 (t) REVERT: B 640 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8129 (mm-40) REVERT: B 651 ASN cc_start: 0.6846 (m110) cc_final: 0.6569 (m110) REVERT: B 660 LEU cc_start: 0.8975 (tp) cc_final: 0.8656 (mp) REVERT: F 99 ASN cc_start: 0.8516 (t0) cc_final: 0.7875 (t0) REVERT: F 142 MET cc_start: 0.8638 (tpp) cc_final: 0.8404 (tpt) REVERT: F 347 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8125 (tppt) REVERT: J 30 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7861 (mtm-85) REVERT: J 39 GLN cc_start: 0.6417 (tp40) cc_final: 0.5902 (tp40) REVERT: J 50 ILE cc_start: 0.8136 (mm) cc_final: 0.7466 (mm) REVERT: J 75 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8019 (ttpt) REVERT: J 89 VAL cc_start: 0.8094 (m) cc_final: 0.7612 (p) REVERT: K 59 PRO cc_start: 0.6494 (Cg_endo) cc_final: 0.5905 (Cg_exo) REVERT: E 99 ASN cc_start: 0.8410 (t0) cc_final: 0.7650 (t0) REVERT: E 161 MET cc_start: 0.8439 (tpp) cc_final: 0.7798 (tpt) REVERT: E 180 ASP cc_start: 0.9017 (m-30) cc_final: 0.8660 (m-30) REVERT: E 274 SER cc_start: 0.9072 (t) cc_final: 0.8861 (t) REVERT: E 475 MET cc_start: 0.8649 (mmm) cc_final: 0.8374 (mmm) REVERT: M 30 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7985 (ttm170) REVERT: M 36 TRP cc_start: 0.7949 (m100) cc_final: 0.7648 (m100) REVERT: M 45 LEU cc_start: 0.4326 (pp) cc_final: 0.4109 (pp) REVERT: M 50 ILE cc_start: 0.7750 (mm) cc_final: 0.7159 (mm) REVERT: N 61 ARG cc_start: 0.7488 (ptt180) cc_final: 0.7160 (ptt-90) REVERT: N 74 LYS cc_start: 0.8534 (mtmt) cc_final: 0.7809 (ttpp) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1249 time to fit residues: 78.2876 Evaluate side-chains 317 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 91 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 652 GLN G 99 ASN G 478 ASN J 5 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090699 restraints weight = 39173.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.092781 restraints weight = 27980.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093504 restraints weight = 22394.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094458 restraints weight = 18878.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094814 restraints weight = 17124.654| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21072 Z= 0.122 Angle : 0.673 10.432 28857 Z= 0.312 Chirality : 0.048 0.279 3480 Planarity : 0.004 0.058 3483 Dihedral : 8.283 115.841 4827 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2370 helix: 1.59 (0.28), residues: 399 sheet: -0.40 (0.21), residues: 600 loop : -1.39 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 298 TYR 0.023 0.001 TYR E 217 PHE 0.014 0.001 PHE H 78 TRP 0.038 0.001 TRP J 36 HIS 0.006 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20919) covalent geometry : angle 0.63106 / 0.30 (28443) SS BOND : bond 0.00412 / 0.27 ( 45) SS BOND : angle 1.68812 / 1.13 ( 90) hydrogen bonds : bond 0.02920 / 1.96 ( 624) hydrogen bonds : angle 4.94634 / 3.47 ( 1620) link_ALPHA1-3 : bond 0.01220 / 0.65 ( 6) link_ALPHA1-3 : angle 2.16433 / 1.25 ( 18) link_ALPHA1-6 : bond 0.01261 / 0.65 ( 6) link_ALPHA1-6 : angle 1.79424 / 0.97 ( 18) link_BETA1-4 : bond 0.00744 / 0.52 ( 39) link_BETA1-4 : angle 2.34252 / 1.61 ( 117) link_NAG-ASN : bond 0.00299 / 0.20 ( 57) link_NAG-ASN : angle 2.01200 / 1.41 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 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: 0 poor density : 384 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8837 (m) cc_final: 0.8434 (t) REVERT: C 633 LYS cc_start: 0.8429 (tppt) cc_final: 0.8123 (tppt) REVERT: G 142 MET cc_start: 0.8859 (tpp) cc_final: 0.8551 (tpt) REVERT: G 161 MET cc_start: 0.8576 (tpp) cc_final: 0.7923 (tpt) REVERT: G 180 ASP cc_start: 0.9047 (m-30) cc_final: 0.8719 (m-30) REVERT: G 274 SER cc_start: 0.8970 (t) cc_final: 0.8715 (t) REVERT: H 30 ARG cc_start: 0.8407 (mtt90) cc_final: 0.7467 (mtm-85) REVERT: H 36 TRP cc_start: 0.7894 (m100) cc_final: 0.7306 (m100) REVERT: H 89 VAL cc_start: 0.7801 (m) cc_final: 0.7372 (p) REVERT: H 91 TYR cc_start: 0.8350 (m-10) cc_final: 0.7650 (m-10) REVERT: L 50 LYS cc_start: 0.6786 (mttt) cc_final: 0.5530 (tmtt) REVERT: B 534 SER cc_start: 0.8893 (m) cc_final: 0.8451 (t) REVERT: B 538 THR cc_start: 0.8929 (p) cc_final: 0.8432 (t) REVERT: B 660 LEU cc_start: 0.8996 (tp) cc_final: 0.8645 (mp) REVERT: F 99 ASN cc_start: 0.8539 (t0) cc_final: 0.7937 (t0) REVERT: F 142 MET cc_start: 0.8624 (tpp) cc_final: 0.8344 (tpt) REVERT: F 161 MET cc_start: 0.8402 (tpp) cc_final: 0.8181 (tpt) REVERT: J 30 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7829 (mtm-85) REVERT: J 39 GLN cc_start: 0.6373 (tp40) cc_final: 0.5861 (tp40) REVERT: J 50 ILE cc_start: 0.8140 (mm) cc_final: 0.7348 (mm) REVERT: J 51 ILE cc_start: 0.8340 (tp) cc_final: 0.7934 (tp) REVERT: J 75 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8034 (ttpt) REVERT: J 89 VAL cc_start: 0.8168 (m) cc_final: 0.7715 (p) REVERT: A 653 GLN cc_start: 0.7695 (mt0) cc_final: 0.7431 (mm-40) REVERT: E 161 MET cc_start: 0.8455 (tpp) cc_final: 0.7802 (tpt) REVERT: E 475 MET cc_start: 0.8613 (mmm) cc_final: 0.8288 (mmm) REVERT: M 30 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8003 (ttm170) REVERT: M 36 TRP cc_start: 0.8034 (m100) cc_final: 0.7828 (m100) REVERT: M 50 ILE cc_start: 0.7790 (mm) cc_final: 0.7060 (mm) REVERT: N 74 LYS cc_start: 0.8550 (mtmt) cc_final: 0.7793 (ttpp) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1177 time to fit residues: 72.4471 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 163 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.3504 r_free = 0.3504 target = 0.120149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088936 restraints weight = 39481.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091259 restraints weight = 27367.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092307 restraints weight = 21412.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093420 restraints weight = 17352.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093643 restraints weight = 15687.780| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21072 Z= 0.141 Angle : 0.684 9.531 28857 Z= 0.318 Chirality : 0.049 0.289 3480 Planarity : 0.004 0.057 3483 Dihedral : 8.244 115.632 4827 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.20 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2370 helix: 1.52 (0.28), residues: 399 sheet: -0.43 (0.21), residues: 600 loop : -1.35 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 298 TYR 0.025 0.001 TYR L 49 PHE 0.016 0.001 PHE H 78 TRP 0.041 0.002 TRP J 36 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (20919) covalent geometry : angle 0.64121 / 0.31 (28443) SS BOND : bond 0.00426 / 0.28 ( 45) SS BOND : angle 1.86343 / 1.27 ( 90) hydrogen bonds : bond 0.02946 / 1.98 ( 624) hydrogen bonds : angle 4.95774 / 3.49 ( 1620) link_ALPHA1-3 : bond 0.01190 / 0.64 ( 6) link_ALPHA1-3 : angle 2.19180 / 1.28 ( 18) link_ALPHA1-6 : bond 0.01243 / 0.64 ( 6) link_ALPHA1-6 : angle 1.84111 / 1.00 ( 18) link_BETA1-4 : bond 0.00730 / 0.51 ( 39) link_BETA1-4 : angle 2.35180 / 1.62 ( 117) link_NAG-ASN : bond 0.00297 / 0.20 ( 57) link_NAG-ASN : angle 2.02986 / 1.43 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 534 SER cc_start: 0.8864 (m) cc_final: 0.8437 (t) REVERT: C 538 THR cc_start: 0.8848 (p) cc_final: 0.8625 (t) REVERT: C 633 LYS cc_start: 0.8462 (tppt) cc_final: 0.8156 (tppt) REVERT: C 658 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8334 (tm-30) REVERT: G 67 ASN cc_start: 0.8913 (t0) cc_final: 0.8688 (t0) REVERT: G 161 MET cc_start: 0.8584 (tpp) cc_final: 0.7874 (tpt) REVERT: G 180 ASP cc_start: 0.9032 (m-30) cc_final: 0.8675 (m-30) REVERT: G 274 SER cc_start: 0.8981 (t) cc_final: 0.8746 (t) REVERT: H 30 ARG cc_start: 0.8436 (mtt90) cc_final: 0.7494 (mtm-85) REVERT: H 89 VAL cc_start: 0.7757 (m) cc_final: 0.7337 (p) REVERT: L 49 TYR cc_start: 0.5612 (p90) cc_final: 0.5321 (p90) REVERT: B 534 SER cc_start: 0.8931 (m) cc_final: 0.8464 (t) REVERT: B 538 THR cc_start: 0.8843 (p) cc_final: 0.8400 (t) REVERT: B 640 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8140 (mm-40) REVERT: B 647 GLU cc_start: 0.6833 (tp30) cc_final: 0.6395 (tp30) REVERT: B 649 SER cc_start: 0.8463 (t) cc_final: 0.8260 (t) REVERT: B 658 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8441 (tm-30) REVERT: B 660 LEU cc_start: 0.8998 (tp) cc_final: 0.8708 (mp) REVERT: F 99 ASN cc_start: 0.8627 (t0) cc_final: 0.7930 (t0) REVERT: F 161 MET cc_start: 0.8429 (tpp) cc_final: 0.8204 (tpt) REVERT: J 30 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7801 (mtm-85) REVERT: J 39 GLN cc_start: 0.6409 (tp40) cc_final: 0.6021 (tp40) REVERT: J 51 ILE cc_start: 0.8310 (tp) cc_final: 0.7989 (tp) REVERT: J 89 VAL cc_start: 0.8175 (m) cc_final: 0.7814 (p) REVERT: A 577 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 653 GLN cc_start: 0.7740 (mt0) cc_final: 0.7415 (mm-40) REVERT: E 161 MET cc_start: 0.8438 (tpp) cc_final: 0.7891 (tpt) REVERT: E 274 SER cc_start: 0.9078 (t) cc_final: 0.8848 (t) REVERT: M 30 ARG cc_start: 0.8518 (mtt90) cc_final: 0.7967 (ttm170) REVERT: N 49 TYR cc_start: 0.5792 (p90) cc_final: 0.5277 (p90) REVERT: N 74 LYS cc_start: 0.8564 (mtmt) cc_final: 0.7790 (ttpp) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.1168 time to fit residues: 72.3060 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 186 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 214 optimal weight: 0.4980 chunk 217 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.3444 r_free = 0.3444 target = 0.115818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.084131 restraints weight = 39913.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086156 restraints weight = 27871.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087526 restraints weight = 21815.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088331 restraints weight = 18465.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088948 restraints weight = 16560.146| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21072 Z= 0.207 Angle : 0.758 9.681 28857 Z= 0.357 Chirality : 0.050 0.335 3480 Planarity : 0.005 0.075 3483 Dihedral : 8.376 116.347 4827 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.71 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.17), residues: 2370 helix: 1.72 (0.28), residues: 378 sheet: -0.52 (0.20), residues: 624 loop : -1.40 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 94 TYR 0.029 0.002 TYR J 33 PHE 0.019 0.002 PHE H 78 TRP 0.050 0.002 TRP J 36 HIS 0.003 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (20919) covalent geometry : angle 0.71228 / 0.35 (28443) SS BOND : bond 0.00602 / 0.40 ( 45) SS BOND : angle 2.31603 / 1.65 ( 90) hydrogen bonds : bond 0.03329 / 2.24 ( 624) hydrogen bonds : angle 5.12648 / 3.62 ( 1620) link_ALPHA1-3 : bond 0.00991 / 0.54 ( 6) link_ALPHA1-3 : angle 2.39471 / 1.41 ( 18) link_ALPHA1-6 : bond 0.01257 / 0.64 ( 6) link_ALPHA1-6 : angle 1.75900 / 0.99 ( 18) link_BETA1-4 : bond 0.00742 / 0.53 ( 39) link_BETA1-4 : angle 2.47555 / 1.71 ( 117) link_NAG-ASN : bond 0.00338 / 0.22 ( 57) link_NAG-ASN : angle 2.17906 / 1.53 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.11 seconds wall clock time: 55 minutes 35.87 seconds (3335.87 seconds total)