Starting phenix.real_space_refine on Sat Jul 4 14:10:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yhs_72972/07_2026/9yhs_72972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yhs_72972/07_2026/9yhs_72972.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/9yhs_72972/07_2026/9yhs_72972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yhs_72972/07_2026/9yhs_72972.map" model { file = "/net/cci-nas-00/data/ceres_data/9yhs_72972/07_2026/9yhs_72972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yhs_72972/07_2026/9yhs_72972.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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 12909 2.51 5 N 3399 2.21 5 O 4260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20691 Number of models: 1 Model: "" Number of chains: 54 Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "L" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 101} Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 101} Chain: "M" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "N" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 101} Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "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: "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: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.03, per 1000 atoms: 0.24 Number of scatterers: 20691 At special positions: 0 Unit cell: (157.47, 161.82, 127.89, 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 4260 8.00 N 3399 7.00 C 12909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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 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 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 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 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 F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 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 G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 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 A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 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 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 T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " " BMA l 3 " - " MAN l 4 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 5 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " GLC S 5 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 5 " " BMA d 3 " - " GLC d 5 " " BMA e 3 " - " MAN e 6 " " BMA l 3 " - " MAN l 5 " " BMA o 3 " - " GLC o 5 " " BMA p 3 " - " MAN p 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 T 2 " - " BMA T 3 " " 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 X 2 " - " BMA X 3 " " 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 e 2 " - " BMA e 3 " " 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 i 2 " - " BMA i 3 " " 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 p 2 " - " BMA p 3 " " 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 A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG D 1 " - " ASN F 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 241 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 344 " " NAG E 608 " - " ASN E 355 " " 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 241 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 344 " " NAG F 608 " - " ASN F 355 " " 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 241 " " NAG G 606 " - " ASN G 339 " " NAG G 607 " - " ASN G 344 " " NAG G 608 " - " ASN G 355 " " NAG I 1 " - " ASN F 160 " " NAG K 700 " - " ASN K 70 " " NAG L 700 " - " ASN L 70 " " NAG N 700 " - " ASN N 70 " " NAG O 1 " - " ASN F 234 " " NAG P 1 " - " ASN F 262 " " NAG Q 1 " - " ASN F 276 " " NAG R 1 " - " ASN F 295 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 386 " " NAG V 1 " - " ASN F 392 " " NAG W 1 " - " ASN F 448 " " NAG X 1 " - " ASN G 156 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 276 " " NAG c 1 " - " ASN G 295 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN G 332 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 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 301 " " NAG p 1 " - " ASN E 332 " " NAG q 1 " - " ASN E 386 " " NAG r 1 " - " ASN E 392 " " NAG s 1 " - " ASN E 448 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 752.0 milliseconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 21.7% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.879A pdb=" N ARG H 66 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.066A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 removed outlier: 3.879A pdb=" N ARG J 66 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL J 67 " --> pdb=" O LYS J 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 63 through 67' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.066A pdb=" N VAL K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 67 removed outlier: 3.879A pdb=" N ARG M 66 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL M 67 " --> pdb=" O LYS M 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 63 through 67' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.066A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.592A 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 543 removed outlier: 3.905A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.988A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.592A 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 543 removed outlier: 3.905A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.989A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 97 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.268A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.648A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.085A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 97 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.268A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.649A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.086A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.592A 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 543 removed outlier: 3.904A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 650 Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.988A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.269A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.649A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.086A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.002A pdb=" N TRP H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR H 21 " --> pdb=" O TRP H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 50 removed outlier: 6.491A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.562A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 3 through 7 removed outlier: 4.003A pdb=" N TRP J 7 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR J 21 " --> pdb=" O TRP J 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'J' and resid 46 through 50 removed outlier: 6.491A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.561A pdb=" N VAL K 104 " --> pdb=" O GLY K 84 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 3 through 7 removed outlier: 4.002A pdb=" N TRP M 7 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR M 21 " --> pdb=" O TRP M 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'M' and resid 46 through 50 removed outlier: 6.490A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.562A pdb=" N VAL N 104 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.653A pdb=" N THR B 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL F 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL B 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 603 through 609 removed outlier: 7.658A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.774A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.777A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AC3, first strand: chain 'F' and resid 157 through 162 Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.448A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 300 through 307 removed outlier: 3.853A pdb=" N THR F 303 " --> pdb=" O ASP F 321A" (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS F 305 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 331 through 334 removed outlier: 3.635A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU F 416 " --> pdb=" O CYS F 331 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AC9, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.775A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.778A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AD4, first strand: chain 'G' and resid 157 through 162 Processing sheet with id=AD5, first strand: chain 'G' and resid 259 through 261 Processing sheet with id=AD6, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.448A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 300 through 307 removed outlier: 3.854A pdb=" N THR G 303 " --> pdb=" O ASP G 321A" (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP G 321A" --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 331 through 334 removed outlier: 3.636A pdb=" N CYS G 331 " --> pdb=" O LEU G 416 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 416 " --> pdb=" O CYS G 331 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 374 through 378 Processing sheet with id=AE1, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AE2, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.657A pdb=" N THR A 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL E 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.774A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.778A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AE6, first strand: chain 'E' and resid 157 through 162 Processing sheet with id=AE7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AE8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.447A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 300 through 307 removed outlier: 3.854A pdb=" N THR E 303 " --> pdb=" O ASP E 321A" (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 331 through 334 removed outlier: 3.635A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AF3, first strand: chain 'E' and resid 423 through 424 588 hydrogen bonds defined for protein. 1521 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: 4.19 Time building geometry restraints manager: 2.77 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: 6396 1.34 - 1.47: 5397 1.47 - 1.59: 9162 1.59 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 21117 Sorted by residual: bond pdb=" C3 NAG G 608 " pdb=" O3 NAG G 608 " ideal model delta sigma weight residual 1.403 1.440 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C3 NAG E 608 " pdb=" O3 NAG E 608 " ideal model delta sigma weight residual 1.403 1.439 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C3 NAG F 608 " pdb=" O3 NAG F 608 " ideal model delta sigma weight residual 1.403 1.439 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C3 NAG C 702 " pdb=" O3 NAG C 702 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C3 NAG A 702 " pdb=" O3 NAG A 702 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.87e+00 ... (remaining 21112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 27504 1.67 - 3.35: 952 3.35 - 5.02: 206 5.02 - 6.70: 33 6.70 - 8.37: 27 Bond angle restraints: 28722 Sorted by residual: angle pdb=" C1 BMA o 3 " pdb=" O5 BMA o 3 " pdb=" C5 BMA o 3 " ideal model delta sigma weight residual 118.82 110.45 8.37 3.00e+00 1.11e-01 7.79e+00 angle pdb=" C1 BMA d 3 " pdb=" O5 BMA d 3 " pdb=" C5 BMA d 3 " ideal model delta sigma weight residual 118.82 110.46 8.36 3.00e+00 1.11e-01 7.77e+00 angle pdb=" C1 BMA S 3 " pdb=" O5 BMA S 3 " pdb=" C5 BMA S 3 " ideal model delta sigma weight residual 118.82 110.48 8.34 3.00e+00 1.11e-01 7.73e+00 angle pdb=" C1 BMA P 3 " pdb=" O5 BMA P 3 " pdb=" C5 BMA P 3 " ideal model delta sigma weight residual 118.82 110.65 8.17 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C1 BMA l 3 " pdb=" O5 BMA l 3 " pdb=" C5 BMA l 3 " ideal model delta sigma weight residual 118.82 110.67 8.15 3.00e+00 1.11e-01 7.38e+00 ... (remaining 28717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 13341 24.30 - 48.61: 763 48.61 - 72.91: 122 72.91 - 97.22: 78 97.22 - 121.52: 84 Dihedral angle restraints: 14388 sinusoidal: 7458 harmonic: 6930 Sorted by residual: dihedral pdb=" CB CYS F 201 " pdb=" SG CYS F 201 " pdb=" SG CYS F 433 " pdb=" CB CYS F 433 " ideal model delta sinusoidal sigma weight residual -86.00 -146.88 60.88 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 -146.88 60.88 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -146.83 60.83 1 1.00e+01 1.00e-02 4.92e+01 ... (remaining 14385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 3603 1.018 - 2.036: 0 2.036 - 3.054: 0 3.054 - 4.072: 0 4.072 - 5.090: 9 Chirality restraints: 3612 Sorted by residual: 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 2.56 -5.09 2.00e-01 2.50e+01 6.48e+02 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 2.56 -5.09 2.00e-01 2.50e+01 6.48e+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 2.56 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 3609 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 295 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C ASN F 295 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN F 295 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS F 296 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 295 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ASN E 295 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN E 295 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS E 296 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 295 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ASN G 295 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN G 295 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS G 296 " -0.012 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11228 2.99 - 3.47: 19705 3.47 - 3.94: 32376 3.94 - 4.42: 36432 4.42 - 4.90: 58814 Nonbonded interactions: 158555 Sorted by model distance: nonbonded pdb=" O5 BMA o 3 " pdb=" O6 BMA o 3 " model vdw 2.511 2.432 nonbonded pdb=" O5 BMA S 3 " pdb=" O6 BMA S 3 " model vdw 2.511 2.432 nonbonded pdb=" O5 BMA d 3 " pdb=" O6 BMA d 3 " model vdw 2.511 2.432 nonbonded pdb=" O LYS K 50 " pdb=" O3 MAN T 5 " model vdw 2.546 3.040 nonbonded pdb=" ND2 ASN F 355 " pdb=" N2 NAG F 608 " model vdw 2.572 2.560 ... (remaining 158550 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 'X' selection = chain 'i' } 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 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' } 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) } ncs_group { reference = chain 'T' selection = chain 'e' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.950 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.037 21297 Z= 0.263 Angle : 0.851 20.231 29217 Z= 0.341 Chirality : 0.258 5.090 3612 Planarity : 0.003 0.037 3477 Dihedral : 18.467 121.522 9795 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.85 % Allowed : 5.74 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.76 (0.17), residues: 2361 helix: 1.60 (0.28), residues: 411 sheet: -0.34 (0.23), residues: 555 loop : -1.27 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 617 TYR 0.011 0.001 TYR J 47 PHE 0.009 0.001 PHE F 159 TRP 0.009 0.001 TRP E 112 HIS 0.003 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.26 (21117) covalent geometry : angle 0.75496 / 0.32 (28722) SS BOND : bond 0.00580 / 0.37 ( 45) SS BOND : angle 1.30782 / 0.83 ( 90) hydrogen bonds : bond 0.14773 / 10.05 ( 588) hydrogen bonds : angle 6.73092 / 4.56 ( 1521) link_ALPHA1-3 : bond 0.00151 / 0.07 ( 12) link_ALPHA1-3 : angle 1.41524 / 0.76 ( 36) link_ALPHA1-6 : bond 0.00222 / 0.12 ( 9) link_ALPHA1-6 : angle 0.96584 / 0.60 ( 27) link_BETA1-4 : bond 0.00455 / 0.28 ( 45) link_BETA1-4 : angle 1.34772 / 0.91 ( 135) link_NAG-ASN : bond 0.00426 / 0.27 ( 69) link_NAG-ASN : angle 4.55161 / 2.92 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 768 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8252 (ptm-80) cc_final: 0.7821 (ttm110) REVERT: L 27 ASP cc_start: 0.9031 (t0) cc_final: 0.8780 (t70) REVERT: L 35 TRP cc_start: 0.8678 (m100) cc_final: 0.8442 (m-10) REVERT: L 100 GLN cc_start: 0.8435 (pp30) cc_final: 0.7571 (pp30) REVERT: J 38 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8153 (ttm110) REVERT: K 78 VAL cc_start: 0.7952 (t) cc_final: 0.7720 (t) REVERT: K 100 GLN cc_start: 0.8156 (pp30) cc_final: 0.7875 (pp30) REVERT: M 38 ARG cc_start: 0.8534 (ptm-80) cc_final: 0.8099 (ttm170) REVERT: M 100 TRP cc_start: 0.9215 (p90) cc_final: 0.8789 (p90) REVERT: N 18 PRO cc_start: 0.8249 (Cg_endo) cc_final: 0.7992 (Cg_exo) REVERT: N 27 ASP cc_start: 0.8630 (t0) cc_final: 0.8106 (t70) REVERT: N 31 THR cc_start: 0.9367 (m) cc_final: 0.9160 (p) REVERT: B 523 LEU cc_start: 0.9199 (mt) cc_final: 0.8718 (mt) REVERT: B 534 SER cc_start: 0.9417 (m) cc_final: 0.9055 (m) REVERT: B 536 THR cc_start: 0.9224 (t) cc_final: 0.8264 (t) REVERT: B 540 GLN cc_start: 0.8295 (mp10) cc_final: 0.7588 (mp10) REVERT: B 590 GLN cc_start: 0.8961 (tp40) cc_final: 0.8295 (tm-30) REVERT: B 591 GLN cc_start: 0.9274 (tm-30) cc_final: 0.9051 (tm-30) REVERT: B 603 ILE cc_start: 0.8958 (mm) cc_final: 0.8701 (pt) REVERT: B 619 LEU cc_start: 0.9122 (tp) cc_final: 0.8888 (tt) REVERT: B 635 ILE cc_start: 0.9653 (pt) cc_final: 0.9143 (pt) REVERT: B 647 GLU cc_start: 0.8439 (tp30) cc_final: 0.8069 (tp30) REVERT: B 652 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7630 (mm110) REVERT: C 534 SER cc_start: 0.9305 (m) cc_final: 0.8895 (m) REVERT: C 577 GLN cc_start: 0.8934 (tt0) cc_final: 0.8655 (tp40) REVERT: C 590 GLN cc_start: 0.8944 (tp40) cc_final: 0.7901 (tm-30) REVERT: C 591 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 595 ILE cc_start: 0.9288 (mm) cc_final: 0.8842 (mm) REVERT: C 635 ILE cc_start: 0.9732 (pt) cc_final: 0.9213 (pt) REVERT: C 650 GLN cc_start: 0.6273 (tp40) cc_final: 0.5783 (tp40) REVERT: C 652 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7562 (mm110) REVERT: C 655 LYS cc_start: 0.8477 (tppt) cc_final: 0.7854 (tppt) REVERT: F 117 LYS cc_start: 0.8752 (tppt) cc_final: 0.8501 (ttpt) REVERT: F 207 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8295 (ptmm) REVERT: F 261 LEU cc_start: 0.9588 (mp) cc_final: 0.9366 (mp) REVERT: F 323 ILE cc_start: 0.8815 (tp) cc_final: 0.8363 (mm) REVERT: F 370 GLU cc_start: 0.8854 (mp0) cc_final: 0.7760 (mp0) REVERT: G 129 LEU cc_start: 0.9234 (mt) cc_final: 0.9008 (mp) REVERT: G 180 ASP cc_start: 0.9117 (m-30) cc_final: 0.8886 (m-30) REVERT: G 275 GLU cc_start: 0.8461 (tt0) cc_final: 0.8226 (tm-30) REVERT: G 300 ASN cc_start: 0.8435 (p0) cc_final: 0.8216 (p0) REVERT: G 377 ASN cc_start: 0.9096 (t0) cc_final: 0.8552 (t0) REVERT: A 590 GLN cc_start: 0.8990 (tp40) cc_final: 0.8318 (tm-30) REVERT: A 591 GLN cc_start: 0.9342 (tm-30) cc_final: 0.8984 (tm-30) REVERT: A 595 ILE cc_start: 0.9478 (mm) cc_final: 0.9247 (mm) REVERT: A 631 TRP cc_start: 0.9240 (t-100) cc_final: 0.8615 (t-100) REVERT: A 634 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8610 (tm-30) REVERT: A 647 GLU cc_start: 0.8342 (tp30) cc_final: 0.7760 (mm-30) REVERT: A 654 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7883 (tm-30) REVERT: E 207 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8262 (ptmm) REVERT: E 213 ILE cc_start: 0.8534 (pt) cc_final: 0.8318 (pt) REVERT: E 275 GLU cc_start: 0.8569 (tt0) cc_final: 0.8235 (tm-30) REVERT: E 325 ASP cc_start: 0.8984 (t0) cc_final: 0.8640 (t0) outliers start: 18 outliers final: 6 residues processed: 783 average time/residue: 0.1374 time to fit residues: 164.9892 Evaluate side-chains 422 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 416 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 9.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 0.5980 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 32 HIS L 37 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 42 GLN ** K 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 HIS B 625 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 203 GLN F 302 ASN G 302 ASN A 540 GLN A 585 HIS A 658 GLN E 302 ASN E 377 ASN E 440 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.070758 restraints weight = 66290.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.073133 restraints weight = 35365.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074715 restraints weight = 23275.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075811 restraints weight = 17539.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076506 restraints weight = 14306.451| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 21297 Z= 0.128 Angle : 0.739 15.449 29217 Z= 0.331 Chirality : 0.049 0.374 3612 Planarity : 0.004 0.069 3477 Dihedral : 12.098 86.038 5349 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Rotamer: Outliers : 0.47 % Allowed : 3.15 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.70 (0.17), residues: 2361 helix: 1.52 (0.27), residues: 417 sheet: -0.42 (0.22), residues: 624 loop : -1.15 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 166 TYR 0.026 0.001 TYR B 643 PHE 0.016 0.002 PHE H 78 TRP 0.013 0.001 TRP A 596 HIS 0.002 0.001 HIS K 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21117) covalent geometry : angle 0.64051 / 0.31 (28722) SS BOND : bond 0.00735 / 0.39 ( 45) SS BOND : angle 2.06505 / 1.36 ( 90) hydrogen bonds : bond 0.03584 / 2.39 ( 588) hydrogen bonds : angle 5.57394 / 3.74 ( 1521) link_ALPHA1-3 : bond 0.00666 / 0.39 ( 12) link_ALPHA1-3 : angle 2.52463 / 1.47 ( 36) link_ALPHA1-6 : bond 0.00400 / 0.24 ( 9) link_ALPHA1-6 : angle 1.72278 / 1.03 ( 27) link_BETA1-4 : bond 0.00480 / 0.31 ( 45) link_BETA1-4 : angle 1.73455 / 1.12 ( 135) link_NAG-ASN : bond 0.00510 / 0.34 ( 69) link_NAG-ASN : angle 3.84552 / 2.46 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 540 time to evaluate : 0.838 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: L 100 GLN cc_start: 0.8355 (pp30) cc_final: 0.7982 (pp30) REVERT: J 77 GLN cc_start: 0.6611 (mm-40) cc_final: 0.6243 (mm-40) REVERT: K 42 GLN cc_start: 0.7358 (mp10) cc_final: 0.6946 (mp10) REVERT: K 78 VAL cc_start: 0.7972 (t) cc_final: 0.7739 (t) REVERT: K 100 GLN cc_start: 0.8142 (pp30) cc_final: 0.7857 (pp30) REVERT: M 100 TRP cc_start: 0.9238 (p90) cc_final: 0.8760 (p90) REVERT: N 27 ASP cc_start: 0.8533 (t0) cc_final: 0.8078 (t70) REVERT: N 42 GLN cc_start: 0.7230 (mp10) cc_final: 0.6558 (mp10) REVERT: B 590 GLN cc_start: 0.9038 (tp40) cc_final: 0.8311 (tm-30) REVERT: B 591 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8780 (tm-30) REVERT: B 630 GLN cc_start: 0.9336 (pm20) cc_final: 0.8755 (pm20) REVERT: B 632 ASP cc_start: 0.8847 (t70) cc_final: 0.8582 (t0) REVERT: B 658 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 590 GLN cc_start: 0.9018 (tp40) cc_final: 0.7924 (tm-30) REVERT: C 591 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8505 (tm-30) REVERT: C 595 ILE cc_start: 0.9183 (mm) cc_final: 0.8682 (mm) REVERT: C 643 TYR cc_start: 0.9418 (m-10) cc_final: 0.9179 (m-80) REVERT: C 652 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7007 (mm110) REVERT: C 655 LYS cc_start: 0.8147 (tppt) cc_final: 0.7822 (tppt) REVERT: C 658 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8077 (tm-30) REVERT: F 95 MET cc_start: 0.8617 (ptt) cc_final: 0.7396 (ppp) REVERT: F 117 LYS cc_start: 0.8621 (tppt) cc_final: 0.8416 (ttpt) REVERT: F 207 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8380 (ptmm) REVERT: F 321 ASP cc_start: 0.7894 (t0) cc_final: 0.7307 (t0) REVERT: F 368 ASP cc_start: 0.7332 (t0) cc_final: 0.6420 (t0) REVERT: F 370 GLU cc_start: 0.8182 (mp0) cc_final: 0.7889 (mp0) REVERT: F 475 MET cc_start: 0.8430 (mmm) cc_final: 0.8137 (mmm) REVERT: G 95 MET cc_start: 0.9119 (ptm) cc_final: 0.7597 (ppp) REVERT: G 180 ASP cc_start: 0.9155 (m-30) cc_final: 0.8914 (m-30) REVERT: G 225 ILE cc_start: 0.9574 (mp) cc_final: 0.9347 (mm) REVERT: G 275 GLU cc_start: 0.8506 (tt0) cc_final: 0.8279 (tm-30) REVERT: G 300 ASN cc_start: 0.8522 (p0) cc_final: 0.8149 (p0) REVERT: G 325 ASP cc_start: 0.8332 (t0) cc_final: 0.8075 (t0) REVERT: G 377 ASN cc_start: 0.9101 (t0) cc_final: 0.8494 (t0) REVERT: G 474 ASP cc_start: 0.8517 (t0) cc_final: 0.8287 (t70) REVERT: G 482 GLU cc_start: 0.8408 (tp30) cc_final: 0.8047 (tp30) REVERT: G 490 LYS cc_start: 0.9306 (ttpt) cc_final: 0.9088 (ttmt) REVERT: A 543 ASN cc_start: 0.8395 (t0) cc_final: 0.7990 (t0) REVERT: A 590 GLN cc_start: 0.8942 (tp40) cc_final: 0.8345 (tm-30) REVERT: A 591 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 595 ILE cc_start: 0.9377 (mm) cc_final: 0.9075 (mm) REVERT: A 607 ASN cc_start: 0.8652 (m-40) cc_final: 0.8380 (m-40) REVERT: A 631 TRP cc_start: 0.9312 (t-100) cc_final: 0.8757 (t-100) REVERT: A 635 ILE cc_start: 0.9674 (pt) cc_final: 0.9335 (tp) REVERT: A 650 GLN cc_start: 0.6787 (tp40) cc_final: 0.6371 (tp40) REVERT: E 95 MET cc_start: 0.8862 (ptt) cc_final: 0.8478 (ppp) REVERT: E 104 MET cc_start: 0.9320 (ttm) cc_final: 0.8109 (tpp) REVERT: E 207 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8285 (ptmm) REVERT: E 213 ILE cc_start: 0.8501 (pt) cc_final: 0.8301 (pt) REVERT: E 275 GLU cc_start: 0.8517 (tt0) cc_final: 0.8246 (tm-30) REVERT: E 325 ASP cc_start: 0.8830 (t0) cc_final: 0.8520 (t0) REVERT: E 474 ASP cc_start: 0.8312 (t0) cc_final: 0.8061 (t70) outliers start: 10 outliers final: 4 residues processed: 547 average time/residue: 0.1313 time to fit residues: 115.2665 Evaluate side-chains 385 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 381 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 207 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 146 optimal weight: 0.0670 chunk 205 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS N 32 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN C 630 GLN F 302 ASN F 440 GLN G 203 GLN G 302 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.069937 restraints weight = 66237.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.072285 restraints weight = 35483.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073875 restraints weight = 23390.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074872 restraints weight = 17567.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075661 restraints weight = 14478.621| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21297 Z= 0.118 Angle : 0.697 14.042 29217 Z= 0.314 Chirality : 0.048 0.418 3612 Planarity : 0.004 0.056 3477 Dihedral : 9.976 65.272 5349 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.70 (0.17), residues: 2361 helix: 1.37 (0.27), residues: 417 sheet: -0.28 (0.22), residues: 603 loop : -1.16 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 166 TYR 0.024 0.001 TYR A 643 PHE 0.014 0.001 PHE F 159 TRP 0.013 0.001 TRP C 596 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21117) covalent geometry : angle 0.61362 / 0.29 (28722) SS BOND : bond 0.00463 / 0.28 ( 45) SS BOND : angle 1.52293 / 0.97 ( 90) hydrogen bonds : bond 0.03194 / 2.12 ( 588) hydrogen bonds : angle 5.40684 / 3.62 ( 1521) link_ALPHA1-3 : bond 0.00912 / 0.54 ( 12) link_ALPHA1-3 : angle 2.22753 / 1.30 ( 36) link_ALPHA1-6 : bond 0.00456 / 0.29 ( 9) link_ALPHA1-6 : angle 1.75629 / 1.04 ( 27) link_BETA1-4 : bond 0.00523 / 0.35 ( 45) link_BETA1-4 : angle 1.66272 / 1.09 ( 135) link_NAG-ASN : bond 0.00570 / 0.38 ( 69) link_NAG-ASN : angle 3.49086 / 2.27 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 509 time to evaluate : 0.748 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: H 77 GLN cc_start: 0.6520 (mm-40) cc_final: 0.6247 (mm-40) REVERT: H 100 ARG cc_start: 0.6602 (ptp90) cc_final: 0.6324 (pmt-80) REVERT: L 100 GLN cc_start: 0.8272 (pp30) cc_final: 0.7866 (pp30) REVERT: J 77 GLN cc_start: 0.6736 (mm-40) cc_final: 0.6304 (mm-40) REVERT: K 42 GLN cc_start: 0.7387 (mp10) cc_final: 0.6893 (mp10) REVERT: K 78 VAL cc_start: 0.8022 (t) cc_final: 0.7727 (t) REVERT: K 100 GLN cc_start: 0.8135 (pp30) cc_final: 0.7863 (pp30) REVERT: M 91 TYR cc_start: 0.8465 (m-80) cc_final: 0.8254 (m-80) REVERT: M 100 TRP cc_start: 0.9308 (p90) cc_final: 0.8791 (p90) REVERT: N 27 ASP cc_start: 0.8649 (t0) cc_final: 0.8328 (t70) REVERT: B 590 GLN cc_start: 0.9031 (tp40) cc_final: 0.8243 (tm-30) REVERT: B 591 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8786 (tm-30) REVERT: B 621 GLU cc_start: 0.8444 (pt0) cc_final: 0.8066 (pt0) REVERT: B 658 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 590 GLN cc_start: 0.8978 (tp40) cc_final: 0.7838 (tm-30) REVERT: C 591 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 595 ILE cc_start: 0.9177 (mm) cc_final: 0.8716 (mm) REVERT: C 630 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.9029 (pm20) REVERT: C 643 TYR cc_start: 0.9367 (m-10) cc_final: 0.9157 (m-80) REVERT: C 647 GLU cc_start: 0.7724 (tp30) cc_final: 0.7365 (tp30) REVERT: C 650 GLN cc_start: 0.6477 (tp40) cc_final: 0.5802 (tp40) REVERT: C 655 LYS cc_start: 0.8141 (tppt) cc_final: 0.7893 (tppt) REVERT: C 658 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8053 (tm-30) REVERT: F 95 MET cc_start: 0.8601 (ptt) cc_final: 0.7667 (ppp) REVERT: F 207 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8345 (ptmm) REVERT: F 368 ASP cc_start: 0.7388 (t0) cc_final: 0.6445 (t0) REVERT: F 370 GLU cc_start: 0.8258 (mp0) cc_final: 0.7868 (mp0) REVERT: G 82 GLN cc_start: 0.7402 (mt0) cc_final: 0.6533 (pm20) REVERT: G 95 MET cc_start: 0.9054 (ptm) cc_final: 0.7547 (ppp) REVERT: G 104 MET cc_start: 0.8923 (tpp) cc_final: 0.8340 (tpp) REVERT: G 180 ASP cc_start: 0.9174 (m-30) cc_final: 0.8905 (m-30) REVERT: G 225 ILE cc_start: 0.9627 (mp) cc_final: 0.9327 (mm) REVERT: G 275 GLU cc_start: 0.8496 (tt0) cc_final: 0.8283 (tm-30) REVERT: G 300 ASN cc_start: 0.8484 (p0) cc_final: 0.8101 (p0) REVERT: G 377 ASN cc_start: 0.9025 (t0) cc_final: 0.8464 (t0) REVERT: A 590 GLN cc_start: 0.8989 (tp40) cc_final: 0.8217 (tm-30) REVERT: A 591 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 595 ILE cc_start: 0.9373 (mm) cc_final: 0.8939 (mm) REVERT: A 607 ASN cc_start: 0.8659 (m-40) cc_final: 0.8403 (m-40) REVERT: A 621 GLU cc_start: 0.8442 (pt0) cc_final: 0.8083 (pt0) REVERT: A 626 MET cc_start: 0.7661 (mtp) cc_final: 0.7456 (mtp) REVERT: A 650 GLN cc_start: 0.6841 (tp40) cc_final: 0.6462 (tp40) REVERT: E 104 MET cc_start: 0.9347 (ttt) cc_final: 0.9000 (tpp) REVERT: E 275 GLU cc_start: 0.8524 (tt0) cc_final: 0.8294 (tm-30) REVERT: E 323 ILE cc_start: 0.9461 (tp) cc_final: 0.9235 (mm) outliers start: 4 outliers final: 0 residues processed: 510 average time/residue: 0.1190 time to fit residues: 98.3695 Evaluate side-chains 379 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 0.0050 chunk 82 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN F 103 GLN F 302 ASN F 348 GLN F 440 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 ASN G 287 GLN G 302 ASN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN E 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.079167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.064218 restraints weight = 67576.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.066477 restraints weight = 36684.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068002 restraints weight = 24538.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069030 restraints weight = 18687.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.069688 restraints weight = 15458.085| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21297 Z= 0.200 Angle : 0.750 13.666 29217 Z= 0.344 Chirality : 0.049 0.393 3612 Planarity : 0.004 0.047 3477 Dihedral : 7.697 57.850 5349 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.71 (0.17), residues: 2361 helix: 1.52 (0.28), residues: 408 sheet: -0.35 (0.22), residues: 570 loop : -1.17 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 100I TYR 0.016 0.002 TYR A 643 PHE 0.029 0.002 PHE E 93 TRP 0.014 0.002 TRP F 96 HIS 0.006 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (21117) covalent geometry : angle 0.66988 / 0.32 (28722) SS BOND : bond 0.00621 / 0.41 ( 45) SS BOND : angle 2.01301 / 1.33 ( 90) hydrogen bonds : bond 0.03254 / 2.16 ( 588) hydrogen bonds : angle 5.38233 / 3.64 ( 1521) link_ALPHA1-3 : bond 0.00851 / 0.49 ( 12) link_ALPHA1-3 : angle 2.13920 / 1.28 ( 36) link_ALPHA1-6 : bond 0.00368 / 0.25 ( 9) link_ALPHA1-6 : angle 2.75352 / 1.72 ( 27) link_BETA1-4 : bond 0.00392 / 0.25 ( 45) link_BETA1-4 : angle 1.79845 / 1.18 ( 135) link_NAG-ASN : bond 0.00500 / 0.35 ( 69) link_NAG-ASN : angle 3.38541 / 2.20 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 464 time to evaluate : 0.498 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: J 77 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6518 (mm-40) REVERT: J 101 ASP cc_start: 0.8575 (t0) cc_final: 0.8053 (m-30) REVERT: K 42 GLN cc_start: 0.7353 (mp10) cc_final: 0.6869 (mp10) REVERT: K 78 VAL cc_start: 0.8154 (t) cc_final: 0.7883 (t) REVERT: K 100 GLN cc_start: 0.8176 (pp30) cc_final: 0.7931 (pp30) REVERT: M 100 TRP cc_start: 0.9441 (p90) cc_final: 0.8911 (p90) REVERT: N 27 ASP cc_start: 0.8851 (t0) cc_final: 0.8634 (t70) REVERT: N 42 GLN cc_start: 0.7117 (mp10) cc_final: 0.6630 (mp10) REVERT: B 590 GLN cc_start: 0.9025 (tp40) cc_final: 0.8203 (tm-30) REVERT: B 591 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8897 (tm-30) REVERT: B 658 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 590 GLN cc_start: 0.9002 (tp40) cc_final: 0.7993 (tm-30) REVERT: C 591 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8915 (tm-30) REVERT: C 643 TYR cc_start: 0.9368 (m-10) cc_final: 0.9115 (m-80) REVERT: C 647 GLU cc_start: 0.7861 (tp30) cc_final: 0.7651 (tp30) REVERT: C 650 GLN cc_start: 0.6761 (tp40) cc_final: 0.6058 (tp40) REVERT: C 652 GLN cc_start: 0.7290 (mm110) cc_final: 0.6647 (mm110) REVERT: C 658 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8373 (tm-30) REVERT: F 67 ASN cc_start: 0.7628 (t0) cc_final: 0.7411 (t0) REVERT: F 104 MET cc_start: 0.9459 (ttt) cc_final: 0.9171 (ttm) REVERT: F 207 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8337 (ptmm) REVERT: F 321 ASP cc_start: 0.7838 (t0) cc_final: 0.7592 (t0) REVERT: F 368 ASP cc_start: 0.7526 (t0) cc_final: 0.6447 (t0) REVERT: F 370 GLU cc_start: 0.8456 (mp0) cc_final: 0.7816 (mp0) REVERT: G 82 GLN cc_start: 0.7479 (mt0) cc_final: 0.6966 (pm20) REVERT: G 95 MET cc_start: 0.9158 (ptm) cc_final: 0.8492 (ppp) REVERT: G 104 MET cc_start: 0.9240 (tpp) cc_final: 0.8966 (tmm) REVERT: G 180 ASP cc_start: 0.9183 (m-30) cc_final: 0.8911 (m-30) REVERT: G 275 GLU cc_start: 0.8586 (tt0) cc_final: 0.8288 (tm-30) REVERT: G 377 ASN cc_start: 0.9129 (t0) cc_final: 0.8618 (t0) REVERT: A 590 GLN cc_start: 0.8990 (tp40) cc_final: 0.8249 (tm-30) REVERT: A 591 GLN cc_start: 0.9326 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 595 ILE cc_start: 0.9435 (mm) cc_final: 0.9008 (mm) REVERT: A 607 ASN cc_start: 0.8668 (m-40) cc_final: 0.8374 (m-40) REVERT: A 650 GLN cc_start: 0.7239 (tp40) cc_final: 0.6600 (tp40) REVERT: E 67 ASN cc_start: 0.7847 (t0) cc_final: 0.7565 (t0) REVERT: E 95 MET cc_start: 0.9110 (ppp) cc_final: 0.8592 (ppp) REVERT: E 104 MET cc_start: 0.9357 (ttt) cc_final: 0.9021 (tpp) REVERT: E 180 ASP cc_start: 0.8888 (m-30) cc_final: 0.8649 (m-30) REVERT: E 275 GLU cc_start: 0.8614 (tt0) cc_final: 0.8332 (tm-30) REVERT: E 325 ASP cc_start: 0.9005 (t0) cc_final: 0.8641 (t0) outliers start: 3 outliers final: 1 residues processed: 465 average time/residue: 0.1213 time to fit residues: 90.8792 Evaluate side-chains 332 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 129 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 136 optimal weight: 0.1980 chunk 182 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 HIS N 37 HIS B 543 ASN B 625 ASN F 440 GLN G 103 GLN G 440 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066659 restraints weight = 66316.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.068989 restraints weight = 35739.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.070567 restraints weight = 23692.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.071624 restraints weight = 17906.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072293 restraints weight = 14762.897| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21297 Z= 0.119 Angle : 0.669 13.250 29217 Z= 0.310 Chirality : 0.047 0.390 3612 Planarity : 0.004 0.042 3477 Dihedral : 7.494 58.027 5349 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.40 % Favored : 95.38 % Rotamer: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2361 helix: 1.54 (0.28), residues: 408 sheet: -0.19 (0.22), residues: 576 loop : -1.18 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 100I TYR 0.022 0.001 TYR B 643 PHE 0.014 0.002 PHE L 98 TRP 0.020 0.001 TRP A 596 HIS 0.003 0.000 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (21117) covalent geometry : angle 0.59721 / 0.29 (28722) SS BOND : bond 0.00547 / 0.35 ( 45) SS BOND : angle 1.85097 / 1.23 ( 90) hydrogen bonds : bond 0.03109 / 2.07 ( 588) hydrogen bonds : angle 5.25477 / 3.56 ( 1521) link_ALPHA1-3 : bond 0.00910 / 0.55 ( 12) link_ALPHA1-3 : angle 2.09748 / 1.23 ( 36) link_ALPHA1-6 : bond 0.00235 / 0.14 ( 9) link_ALPHA1-6 : angle 1.57469 / 0.99 ( 27) link_BETA1-4 : bond 0.00482 / 0.30 ( 45) link_BETA1-4 : angle 1.48492 / 0.98 ( 135) link_NAG-ASN : bond 0.00507 / 0.35 ( 69) link_NAG-ASN : angle 3.12233 / 2.03 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 0.769 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: H 25 TYR cc_start: 0.6908 (m-80) cc_final: 0.6676 (m-80) REVERT: H 101 ASP cc_start: 0.8593 (t0) cc_final: 0.7972 (m-30) REVERT: L 42 GLN cc_start: 0.7268 (mp10) cc_final: 0.6841 (mp10) REVERT: J 52 ILE cc_start: 0.9446 (mp) cc_final: 0.9058 (pt) REVERT: J 77 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6593 (mm-40) REVERT: J 101 ASP cc_start: 0.8549 (t0) cc_final: 0.8069 (m-30) REVERT: K 42 GLN cc_start: 0.7373 (mp10) cc_final: 0.6886 (mp10) REVERT: K 78 VAL cc_start: 0.8125 (t) cc_final: 0.7859 (t) REVERT: K 100 GLN cc_start: 0.8106 (pp30) cc_final: 0.7843 (pp30) REVERT: M 20 LEU cc_start: 0.8399 (tp) cc_final: 0.7779 (mp) REVERT: M 72 ASP cc_start: 0.7511 (t0) cc_final: 0.6995 (p0) REVERT: N 42 GLN cc_start: 0.7180 (mp10) cc_final: 0.6673 (mp10) REVERT: B 575 GLN cc_start: 0.7824 (pm20) cc_final: 0.7306 (pp30) REVERT: B 590 GLN cc_start: 0.9006 (tp40) cc_final: 0.8211 (tm-30) REVERT: B 591 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8931 (tm-30) REVERT: B 621 GLU cc_start: 0.8467 (pt0) cc_final: 0.8111 (pt0) REVERT: B 658 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 590 GLN cc_start: 0.9060 (tp40) cc_final: 0.7882 (tm-30) REVERT: C 591 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8858 (tm-30) REVERT: C 606 THR cc_start: 0.9610 (p) cc_final: 0.9406 (p) REVERT: C 621 GLU cc_start: 0.8341 (pt0) cc_final: 0.7935 (pt0) REVERT: C 643 TYR cc_start: 0.9344 (m-10) cc_final: 0.9041 (m-80) REVERT: C 647 GLU cc_start: 0.7844 (tp30) cc_final: 0.7565 (tp30) REVERT: C 650 GLN cc_start: 0.6643 (tp40) cc_final: 0.6141 (tp40) REVERT: C 652 GLN cc_start: 0.7289 (mm110) cc_final: 0.6706 (mm110) REVERT: C 658 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8056 (tm-30) REVERT: F 104 MET cc_start: 0.9482 (ttt) cc_final: 0.9173 (ttm) REVERT: F 207 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8315 (ptmm) REVERT: F 321 ASP cc_start: 0.7878 (t0) cc_final: 0.7605 (t0) REVERT: G 82 GLN cc_start: 0.7504 (mt0) cc_final: 0.6886 (pm20) REVERT: G 95 MET cc_start: 0.9099 (ptm) cc_final: 0.8404 (ppp) REVERT: G 122 LEU cc_start: 0.9475 (mp) cc_final: 0.8820 (pp) REVERT: G 180 ASP cc_start: 0.9184 (m-30) cc_final: 0.8919 (m-30) REVERT: G 275 GLU cc_start: 0.8562 (tt0) cc_final: 0.8263 (tm-30) REVERT: G 377 ASN cc_start: 0.8955 (t0) cc_final: 0.8449 (t0) REVERT: A 540 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8594 (mm-40) REVERT: A 590 GLN cc_start: 0.8968 (tp40) cc_final: 0.8164 (tm-30) REVERT: A 591 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 595 ILE cc_start: 0.9293 (mm) cc_final: 0.8871 (mm) REVERT: A 607 ASN cc_start: 0.8614 (m-40) cc_final: 0.8232 (m-40) REVERT: A 650 GLN cc_start: 0.6965 (tp40) cc_final: 0.6417 (tp40) REVERT: E 161 MET cc_start: 0.9103 (tpp) cc_final: 0.8822 (tpp) REVERT: E 275 GLU cc_start: 0.8611 (tt0) cc_final: 0.8279 (tm-30) REVERT: E 325 ASP cc_start: 0.8810 (t0) cc_final: 0.8342 (t0) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.1218 time to fit residues: 98.5415 Evaluate side-chains 348 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 625 ASN F 103 GLN F 440 GLN G 103 GLN G 440 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS E 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.066278 restraints weight = 65967.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.068569 restraints weight = 35561.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.070101 restraints weight = 23665.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071150 restraints weight = 18016.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071841 restraints weight = 14859.699| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21297 Z= 0.117 Angle : 0.661 13.184 29217 Z= 0.306 Chirality : 0.047 0.368 3612 Planarity : 0.003 0.040 3477 Dihedral : 7.200 57.207 5349 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.66 (0.18), residues: 2361 helix: 1.49 (0.28), residues: 414 sheet: -0.22 (0.22), residues: 603 loop : -1.19 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.022 0.001 TYR B 643 PHE 0.015 0.001 PHE N 98 TRP 0.022 0.001 TRP B 596 HIS 0.003 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (21117) covalent geometry : angle 0.59283 / 0.29 (28722) SS BOND : bond 0.00338 / 0.22 ( 45) SS BOND : angle 1.67680 / 1.11 ( 90) hydrogen bonds : bond 0.03075 / 2.07 ( 588) hydrogen bonds : angle 5.20722 / 3.54 ( 1521) link_ALPHA1-3 : bond 0.00936 / 0.56 ( 12) link_ALPHA1-3 : angle 2.05612 / 1.20 ( 36) link_ALPHA1-6 : bond 0.00165 / 0.10 ( 9) link_ALPHA1-6 : angle 1.58557 / 1.00 ( 27) link_BETA1-4 : bond 0.00394 / 0.25 ( 45) link_BETA1-4 : angle 1.46446 / 0.97 ( 135) link_NAG-ASN : bond 0.00489 / 0.34 ( 69) link_NAG-ASN : angle 3.04934 / 1.97 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 0.756 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: H 25 TYR cc_start: 0.6967 (m-80) cc_final: 0.6763 (m-80) REVERT: H 52 ILE cc_start: 0.9521 (mp) cc_final: 0.9194 (pt) REVERT: L 42 GLN cc_start: 0.7247 (mp10) cc_final: 0.6817 (mp10) REVERT: J 77 GLN cc_start: 0.7098 (mm-40) cc_final: 0.6659 (mm-40) REVERT: J 101 ASP cc_start: 0.8532 (t0) cc_final: 0.8080 (m-30) REVERT: K 42 GLN cc_start: 0.7409 (mp10) cc_final: 0.6938 (mp10) REVERT: K 78 VAL cc_start: 0.8117 (t) cc_final: 0.7850 (t) REVERT: K 100 GLN cc_start: 0.8075 (pp30) cc_final: 0.7824 (pp30) REVERT: M 20 LEU cc_start: 0.8401 (tp) cc_final: 0.7742 (mp) REVERT: M 72 ASP cc_start: 0.7487 (t0) cc_final: 0.7266 (p0) REVERT: N 42 GLN cc_start: 0.7247 (mp10) cc_final: 0.6718 (mp10) REVERT: B 590 GLN cc_start: 0.9079 (tp40) cc_final: 0.8214 (tm-30) REVERT: B 591 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8872 (tt0) REVERT: B 621 GLU cc_start: 0.8488 (pt0) cc_final: 0.8216 (pt0) REVERT: B 654 GLU cc_start: 0.8025 (pp20) cc_final: 0.7583 (pp20) REVERT: B 658 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 590 GLN cc_start: 0.9055 (tp40) cc_final: 0.7902 (tm-30) REVERT: C 591 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8834 (tm-30) REVERT: C 621 GLU cc_start: 0.8350 (pt0) cc_final: 0.7989 (pt0) REVERT: C 643 TYR cc_start: 0.9317 (m-10) cc_final: 0.8993 (m-80) REVERT: C 647 GLU cc_start: 0.7697 (tp30) cc_final: 0.7390 (tp30) REVERT: C 650 GLN cc_start: 0.6568 (tp40) cc_final: 0.6065 (tp40) REVERT: C 655 LYS cc_start: 0.8501 (tppt) cc_final: 0.8176 (tppt) REVERT: C 658 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 82 GLN cc_start: 0.7606 (mt0) cc_final: 0.7206 (pm20) REVERT: F 104 MET cc_start: 0.9518 (ttt) cc_final: 0.9232 (ttm) REVERT: G 67 ASN cc_start: 0.7982 (t0) cc_final: 0.7642 (t0) REVERT: G 82 GLN cc_start: 0.7466 (mt0) cc_final: 0.6942 (pm20) REVERT: G 95 MET cc_start: 0.9101 (ptm) cc_final: 0.8368 (ppp) REVERT: G 104 MET cc_start: 0.9176 (tpp) cc_final: 0.8756 (tmm) REVERT: G 122 LEU cc_start: 0.9457 (mp) cc_final: 0.8861 (pp) REVERT: G 180 ASP cc_start: 0.9165 (m-30) cc_final: 0.8884 (m-30) REVERT: G 275 GLU cc_start: 0.8557 (tt0) cc_final: 0.8275 (tm-30) REVERT: G 377 ASN cc_start: 0.8887 (t0) cc_final: 0.8467 (t0) REVERT: A 590 GLN cc_start: 0.8957 (tp40) cc_final: 0.8112 (tm-30) REVERT: A 591 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8529 (tm-30) REVERT: A 595 ILE cc_start: 0.9247 (mm) cc_final: 0.8843 (mm) REVERT: A 607 ASN cc_start: 0.8663 (m-40) cc_final: 0.8287 (m-40) REVERT: A 650 GLN cc_start: 0.7054 (tp40) cc_final: 0.6474 (tp40) REVERT: E 67 ASN cc_start: 0.7982 (t0) cc_final: 0.7748 (t0) REVERT: E 104 MET cc_start: 0.9375 (ttt) cc_final: 0.8997 (tpp) REVERT: E 161 MET cc_start: 0.9140 (tpp) cc_final: 0.8843 (tpp) REVERT: E 275 GLU cc_start: 0.8598 (tt0) cc_final: 0.8290 (tm-30) REVERT: E 321 ASP cc_start: 0.7484 (t0) cc_final: 0.7221 (t0) REVERT: E 325 ASP cc_start: 0.8804 (t0) cc_final: 0.8355 (t0) outliers start: 2 outliers final: 0 residues processed: 476 average time/residue: 0.1213 time to fit residues: 95.2510 Evaluate side-chains 347 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 30 optimal weight: 0.0970 chunk 230 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 86 optimal weight: 0.0970 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 625 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 440 GLN G 103 GLN G 440 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 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 = 0.3263 r_free = 0.3263 target = 0.081481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066498 restraints weight = 66515.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.068810 restraints weight = 36041.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070372 restraints weight = 23999.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071422 restraints weight = 18229.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.072169 restraints weight = 15049.200| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21297 Z= 0.112 Angle : 0.649 13.065 29217 Z= 0.300 Chirality : 0.046 0.370 3612 Planarity : 0.004 0.066 3477 Dihedral : 6.924 56.071 5349 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.66 % Favored : 95.17 % Rotamer: Outliers : 0.09 % Allowed : 1.08 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.66 (0.18), residues: 2361 helix: 1.50 (0.28), residues: 414 sheet: -0.16 (0.23), residues: 588 loop : -1.22 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 100I TYR 0.019 0.001 TYR E 134 PHE 0.013 0.001 PHE L 98 TRP 0.019 0.001 TRP A 596 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (21117) covalent geometry : angle 0.58486 / 0.28 (28722) SS BOND : bond 0.00476 / 0.26 ( 45) SS BOND : angle 1.53964 / 1.03 ( 90) hydrogen bonds : bond 0.02967 / 1.98 ( 588) hydrogen bonds : angle 5.14419 / 3.51 ( 1521) link_ALPHA1-3 : bond 0.00912 / 0.55 ( 12) link_ALPHA1-3 : angle 2.04265 / 1.19 ( 36) link_ALPHA1-6 : bond 0.00189 / 0.11 ( 9) link_ALPHA1-6 : angle 1.54112 / 0.97 ( 27) link_BETA1-4 : bond 0.00388 / 0.24 ( 45) link_BETA1-4 : angle 1.42641 / 0.95 ( 135) link_NAG-ASN : bond 0.00499 / 0.34 ( 69) link_NAG-ASN : angle 2.94017 / 1.90 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 0.757 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: H 25 TYR cc_start: 0.6971 (m-80) cc_final: 0.6765 (m-80) REVERT: L 42 GLN cc_start: 0.7316 (mp10) cc_final: 0.6896 (mp10) REVERT: J 52 ILE cc_start: 0.9541 (mp) cc_final: 0.9136 (pt) REVERT: J 77 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6630 (mm-40) REVERT: J 101 ASP cc_start: 0.8529 (t0) cc_final: 0.8139 (m-30) REVERT: K 42 GLN cc_start: 0.7412 (mp10) cc_final: 0.6943 (mp10) REVERT: K 78 VAL cc_start: 0.8144 (t) cc_final: 0.7886 (t) REVERT: K 100 GLN cc_start: 0.8086 (pp30) cc_final: 0.7829 (pp30) REVERT: M 20 LEU cc_start: 0.8408 (tp) cc_final: 0.7740 (mp) REVERT: M 72 ASP cc_start: 0.7941 (t0) cc_final: 0.7339 (p0) REVERT: M 100 MET cc_start: 0.8766 (mmm) cc_final: 0.8487 (tpp) REVERT: N 42 GLN cc_start: 0.7300 (mp10) cc_final: 0.6782 (mp-120) REVERT: B 590 GLN cc_start: 0.9043 (tp40) cc_final: 0.8185 (tm-30) REVERT: B 591 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8942 (tm-30) REVERT: B 621 GLU cc_start: 0.8499 (pt0) cc_final: 0.8255 (pt0) REVERT: B 655 LYS cc_start: 0.8456 (tppt) cc_final: 0.8016 (tppt) REVERT: B 658 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 590 GLN cc_start: 0.9065 (tp40) cc_final: 0.7904 (tm-30) REVERT: C 591 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8849 (tm-30) REVERT: C 607 ASN cc_start: 0.8879 (p0) cc_final: 0.8652 (m-40) REVERT: C 621 GLU cc_start: 0.8336 (pt0) cc_final: 0.7940 (pt0) REVERT: C 643 TYR cc_start: 0.9293 (m-10) cc_final: 0.8988 (m-80) REVERT: C 650 GLN cc_start: 0.6509 (tp40) cc_final: 0.5908 (tp40) REVERT: C 655 LYS cc_start: 0.8561 (tppt) cc_final: 0.8250 (tppt) REVERT: C 658 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8142 (tm-30) REVERT: F 82 GLN cc_start: 0.7607 (mt0) cc_final: 0.7229 (pm20) REVERT: F 207 LYS cc_start: 0.9015 (mmpt) cc_final: 0.8163 (ptmm) REVERT: F 321 ASP cc_start: 0.7817 (t0) cc_final: 0.7347 (t0) REVERT: G 82 GLN cc_start: 0.7490 (mt0) cc_final: 0.6934 (pm20) REVERT: G 95 MET cc_start: 0.9070 (ptm) cc_final: 0.8386 (ppp) REVERT: G 122 LEU cc_start: 0.9448 (mp) cc_final: 0.8737 (pp) REVERT: G 180 ASP cc_start: 0.9179 (m-30) cc_final: 0.8895 (m-30) REVERT: G 275 GLU cc_start: 0.8464 (tt0) cc_final: 0.8219 (tm-30) REVERT: G 377 ASN cc_start: 0.9012 (t0) cc_final: 0.8571 (t0) REVERT: A 590 GLN cc_start: 0.8980 (tp40) cc_final: 0.8077 (tm-30) REVERT: A 591 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 595 ILE cc_start: 0.9217 (mm) cc_final: 0.8808 (mm) REVERT: A 607 ASN cc_start: 0.8675 (m-40) cc_final: 0.8302 (m-40) REVERT: A 650 GLN cc_start: 0.7010 (tp40) cc_final: 0.6392 (tp40) REVERT: E 67 ASN cc_start: 0.8009 (t0) cc_final: 0.7754 (t0) REVERT: E 161 MET cc_start: 0.9164 (tpp) cc_final: 0.8864 (tpp) REVERT: E 275 GLU cc_start: 0.8582 (tt0) cc_final: 0.8255 (tm-30) REVERT: E 321 ASP cc_start: 0.7653 (t0) cc_final: 0.7253 (t0) outliers start: 2 outliers final: 0 residues processed: 464 average time/residue: 0.1215 time to fit residues: 93.1952 Evaluate side-chains 336 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 194 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 625 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS F 103 GLN F 287 GLN F 440 GLN G 103 GLN G 302 ASN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060967 restraints weight = 67520.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063157 restraints weight = 37122.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.064659 restraints weight = 24929.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065665 restraints weight = 19104.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066303 restraints weight = 15925.357| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21297 Z= 0.212 Angle : 0.744 12.789 29217 Z= 0.349 Chirality : 0.048 0.372 3612 Planarity : 0.004 0.042 3477 Dihedral : 7.160 56.345 5349 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 0.14 % Allowed : 1.65 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.87 (0.17), residues: 2361 helix: 1.12 (0.27), residues: 423 sheet: -0.44 (0.22), residues: 597 loop : -1.22 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 100I TYR 0.028 0.002 TYR B 643 PHE 0.013 0.002 PHE G 93 TRP 0.028 0.002 TRP B 596 HIS 0.009 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (21117) covalent geometry : angle 0.67853 / 0.33 (28722) SS BOND : bond 0.00565 / 0.38 ( 45) SS BOND : angle 2.17052 / 1.39 ( 90) hydrogen bonds : bond 0.03335 / 2.28 ( 588) hydrogen bonds : angle 5.31360 / 3.65 ( 1521) link_ALPHA1-3 : bond 0.00740 / 0.45 ( 12) link_ALPHA1-3 : angle 2.20675 / 1.31 ( 36) link_ALPHA1-6 : bond 0.00184 / 0.12 ( 9) link_ALPHA1-6 : angle 1.76829 / 1.15 ( 27) link_BETA1-4 : bond 0.00321 / 0.20 ( 45) link_BETA1-4 : angle 1.60710 / 1.05 ( 135) link_NAG-ASN : bond 0.00547 / 0.39 ( 69) link_NAG-ASN : angle 3.04618 / 1.98 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.756 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: L 42 GLN cc_start: 0.7346 (mp10) cc_final: 0.6884 (mp10) REVERT: J 77 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6694 (mm-40) REVERT: J 101 ASP cc_start: 0.8445 (t0) cc_final: 0.8175 (m-30) REVERT: K 42 GLN cc_start: 0.7409 (mp10) cc_final: 0.6842 (mp10) REVERT: K 78 VAL cc_start: 0.8233 (t) cc_final: 0.7984 (t) REVERT: K 100 GLN cc_start: 0.8112 (pp30) cc_final: 0.7868 (pp30) REVERT: M 52 ILE cc_start: 0.9567 (pt) cc_final: 0.9121 (pt) REVERT: M 72 ASP cc_start: 0.8111 (t0) cc_final: 0.7533 (p0) REVERT: N 42 GLN cc_start: 0.7366 (mp10) cc_final: 0.6852 (mp10) REVERT: B 590 GLN cc_start: 0.9013 (tp40) cc_final: 0.8022 (tm-30) REVERT: B 591 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8787 (tm-30) REVERT: B 607 ASN cc_start: 0.8955 (p0) cc_final: 0.8702 (p0) REVERT: B 621 GLU cc_start: 0.8603 (pt0) cc_final: 0.8212 (pt0) REVERT: B 650 GLN cc_start: 0.6570 (tp40) cc_final: 0.5912 (tp40) REVERT: B 655 LYS cc_start: 0.8698 (tppt) cc_final: 0.8179 (tppt) REVERT: B 658 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 590 GLN cc_start: 0.9050 (tp40) cc_final: 0.8132 (tm-30) REVERT: C 591 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8944 (tm-30) REVERT: C 606 THR cc_start: 0.9603 (p) cc_final: 0.9363 (t) REVERT: C 643 TYR cc_start: 0.9307 (m-10) cc_final: 0.9000 (m-80) REVERT: C 650 GLN cc_start: 0.6841 (tp40) cc_final: 0.6457 (tp40) REVERT: C 655 LYS cc_start: 0.8764 (tppt) cc_final: 0.8377 (tppt) REVERT: C 658 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 67 ASN cc_start: 0.8030 (t0) cc_final: 0.7738 (t0) REVERT: F 82 GLN cc_start: 0.7762 (mt0) cc_final: 0.7378 (pm20) REVERT: F 100 MET cc_start: 0.8677 (mtm) cc_final: 0.8265 (mtp) REVERT: F 142 MET cc_start: 0.8912 (tpp) cc_final: 0.8649 (tpp) REVERT: F 321 ASP cc_start: 0.7903 (t0) cc_final: 0.7505 (t0) REVERT: G 67 ASN cc_start: 0.8009 (t0) cc_final: 0.7764 (t0) REVERT: G 82 GLN cc_start: 0.7609 (mt0) cc_final: 0.7144 (pm20) REVERT: G 95 MET cc_start: 0.9109 (ptm) cc_final: 0.8534 (ppp) REVERT: G 180 ASP cc_start: 0.9154 (m-30) cc_final: 0.8887 (m-30) REVERT: G 275 GLU cc_start: 0.8559 (tt0) cc_final: 0.8347 (tm-30) REVERT: G 377 ASN cc_start: 0.9195 (t0) cc_final: 0.8717 (t0) REVERT: A 595 ILE cc_start: 0.9420 (mm) cc_final: 0.9201 (mm) REVERT: A 607 ASN cc_start: 0.8725 (m-40) cc_final: 0.8387 (m-40) REVERT: A 650 GLN cc_start: 0.7334 (tp40) cc_final: 0.6656 (tp40) REVERT: E 97 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8861 (tppt) REVERT: E 180 ASP cc_start: 0.8964 (m-30) cc_final: 0.8699 (m-30) REVERT: E 275 GLU cc_start: 0.8560 (tt0) cc_final: 0.8298 (tm-30) REVERT: E 321 ASP cc_start: 0.7863 (t0) cc_final: 0.7659 (t0) REVERT: E 325 ASP cc_start: 0.8861 (t0) cc_final: 0.8559 (t0) outliers start: 3 outliers final: 0 residues processed: 434 average time/residue: 0.1237 time to fit residues: 87.7994 Evaluate side-chains 316 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 6 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 0.0670 chunk 127 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 377 ASN F 440 GLN G 103 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.061542 restraints weight = 67134.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063744 restraints weight = 36619.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.065206 restraints weight = 24620.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066265 restraints weight = 18845.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066914 restraints weight = 15645.790| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21297 Z= 0.172 Angle : 0.712 12.590 29217 Z= 0.335 Chirality : 0.048 0.369 3612 Planarity : 0.004 0.040 3477 Dihedral : 7.055 55.448 5349 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.76 % Favored : 94.07 % Rotamer: Outliers : 0.14 % Allowed : 0.42 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.79 (0.17), residues: 2361 helix: 1.22 (0.27), residues: 426 sheet: -0.34 (0.22), residues: 627 loop : -1.23 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 100I TYR 0.026 0.002 TYR B 643 PHE 0.017 0.002 PHE K 98 TRP 0.070 0.002 TRP B 596 HIS 0.006 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (21117) covalent geometry : angle 0.65318 / 0.32 (28722) SS BOND : bond 0.00469 / 0.32 ( 45) SS BOND : angle 1.88826 / 1.22 ( 90) hydrogen bonds : bond 0.03243 / 2.20 ( 588) hydrogen bonds : angle 5.26585 / 3.60 ( 1521) link_ALPHA1-3 : bond 0.00818 / 0.49 ( 12) link_ALPHA1-3 : angle 2.03829 / 1.20 ( 36) link_ALPHA1-6 : bond 0.00190 / 0.11 ( 9) link_ALPHA1-6 : angle 1.60729 / 1.04 ( 27) link_BETA1-4 : bond 0.00339 / 0.22 ( 45) link_BETA1-4 : angle 1.43090 / 0.94 ( 135) link_NAG-ASN : bond 0.00503 / 0.35 ( 69) link_NAG-ASN : angle 2.90579 / 1.89 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 428 time to evaluate : 0.706 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: L 42 GLN cc_start: 0.7380 (mp10) cc_final: 0.6924 (mp10) REVERT: L 100 GLN cc_start: 0.8324 (pp30) cc_final: 0.8050 (pp30) REVERT: J 77 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6746 (mm-40) REVERT: J 101 ASP cc_start: 0.8448 (t0) cc_final: 0.8182 (m-30) REVERT: K 42 GLN cc_start: 0.7448 (mp10) cc_final: 0.6863 (mp10) REVERT: K 78 VAL cc_start: 0.8206 (t) cc_final: 0.7948 (t) REVERT: K 100 GLN cc_start: 0.8113 (pp30) cc_final: 0.7859 (pp30) REVERT: M 52 ILE cc_start: 0.9699 (pt) cc_final: 0.9454 (pt) REVERT: M 72 ASP cc_start: 0.8158 (t0) cc_final: 0.7601 (p0) REVERT: N 42 GLN cc_start: 0.7417 (mp10) cc_final: 0.6925 (mp10) REVERT: B 584 GLU cc_start: 0.9288 (tp30) cc_final: 0.9013 (tp30) REVERT: B 590 GLN cc_start: 0.8952 (tp40) cc_final: 0.8003 (tm-30) REVERT: B 591 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8831 (tm-30) REVERT: B 607 ASN cc_start: 0.8894 (p0) cc_final: 0.8678 (p0) REVERT: B 650 GLN cc_start: 0.6551 (tp40) cc_final: 0.5884 (tp40) REVERT: B 655 LYS cc_start: 0.8674 (tppt) cc_final: 0.8197 (tppt) REVERT: B 658 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8213 (tm-30) REVERT: C 575 GLN cc_start: 0.7565 (pm20) cc_final: 0.7180 (pp30) REVERT: C 590 GLN cc_start: 0.9055 (tp40) cc_final: 0.8224 (tm-30) REVERT: C 591 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8818 (tt0) REVERT: C 607 ASN cc_start: 0.8940 (p0) cc_final: 0.8547 (m-40) REVERT: C 638 TYR cc_start: 0.8593 (m-10) cc_final: 0.8387 (m-10) REVERT: C 643 TYR cc_start: 0.9308 (m-10) cc_final: 0.8945 (m-80) REVERT: C 650 GLN cc_start: 0.6884 (tp40) cc_final: 0.6040 (tp40) REVERT: C 655 LYS cc_start: 0.8757 (tppt) cc_final: 0.8353 (tppt) REVERT: C 658 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8038 (tm-30) REVERT: F 82 GLN cc_start: 0.7763 (mt0) cc_final: 0.7377 (pm20) REVERT: F 321 ASP cc_start: 0.7645 (t0) cc_final: 0.7377 (t0) REVERT: G 67 ASN cc_start: 0.7946 (t0) cc_final: 0.7714 (t0) REVERT: G 82 GLN cc_start: 0.7662 (mt0) cc_final: 0.7176 (pm20) REVERT: G 95 MET cc_start: 0.9126 (ptm) cc_final: 0.8472 (ppp) REVERT: G 104 MET cc_start: 0.8944 (tpp) cc_final: 0.8044 (tpp) REVERT: G 161 MET cc_start: 0.9161 (tpp) cc_final: 0.8828 (tpp) REVERT: G 180 ASP cc_start: 0.9181 (m-30) cc_final: 0.8868 (m-30) REVERT: G 275 GLU cc_start: 0.8569 (tt0) cc_final: 0.8341 (tm-30) REVERT: G 377 ASN cc_start: 0.9115 (t0) cc_final: 0.8669 (t0) REVERT: A 590 GLN cc_start: 0.9005 (tp40) cc_final: 0.8223 (tm-30) REVERT: A 607 ASN cc_start: 0.8684 (m-40) cc_final: 0.8367 (m-40) REVERT: A 650 GLN cc_start: 0.7297 (tp40) cc_final: 0.6549 (tp40) REVERT: A 658 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 97 LYS cc_start: 0.9232 (mmpt) cc_final: 0.8877 (tppt) REVERT: E 122 LEU cc_start: 0.9490 (mt) cc_final: 0.8947 (pp) REVERT: E 180 ASP cc_start: 0.9020 (m-30) cc_final: 0.8765 (m-30) REVERT: E 275 GLU cc_start: 0.8514 (tt0) cc_final: 0.8271 (tm-30) REVERT: E 321 ASP cc_start: 0.7774 (t0) cc_final: 0.7363 (t0) REVERT: E 325 ASP cc_start: 0.8716 (t0) cc_final: 0.8504 (t0) outliers start: 3 outliers final: 0 residues processed: 430 average time/residue: 0.1227 time to fit residues: 86.6192 Evaluate side-chains 317 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 74 optimal weight: 0.0050 chunk 32 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 56 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 625 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 440 GLN G 103 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.061465 restraints weight = 67547.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.063689 restraints weight = 36586.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065204 restraints weight = 24495.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.066240 restraints weight = 18669.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.066917 restraints weight = 15463.508| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21297 Z= 0.156 Angle : 0.707 12.534 29217 Z= 0.331 Chirality : 0.048 0.368 3612 Planarity : 0.004 0.042 3477 Dihedral : 6.939 55.160 5349 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 0.09 % Allowed : 0.33 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.73 (0.17), residues: 2361 helix: 1.17 (0.27), residues: 423 sheet: -0.21 (0.23), residues: 570 loop : -1.17 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 100I TYR 0.026 0.002 TYR B 643 PHE 0.016 0.001 PHE K 98 TRP 0.063 0.002 TRP B 596 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (21117) covalent geometry : angle 0.64778 / 0.32 (28722) SS BOND : bond 0.00435 / 0.30 ( 45) SS BOND : angle 1.89893 / 1.22 ( 90) hydrogen bonds : bond 0.03191 / 2.17 ( 588) hydrogen bonds : angle 5.23243 / 3.57 ( 1521) link_ALPHA1-3 : bond 0.00845 / 0.49 ( 12) link_ALPHA1-3 : angle 2.05050 / 1.20 ( 36) link_ALPHA1-6 : bond 0.00203 / 0.12 ( 9) link_ALPHA1-6 : angle 1.57817 / 1.03 ( 27) link_BETA1-4 : bond 0.00340 / 0.22 ( 45) link_BETA1-4 : angle 1.43629 / 0.95 ( 135) link_NAG-ASN : bond 0.00503 / 0.35 ( 69) link_NAG-ASN : angle 2.88217 / 1.87 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 417 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.8798 (mmm) cc_final: 0.8516 (mmm) REVERT: L 42 GLN cc_start: 0.7390 (mp10) cc_final: 0.6902 (mp10) REVERT: L 100 GLN cc_start: 0.8389 (pp30) cc_final: 0.8111 (pp30) REVERT: J 52 ILE cc_start: 0.9511 (mt) cc_final: 0.9060 (pt) REVERT: J 77 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6785 (mm-40) REVERT: J 101 ASP cc_start: 0.8486 (t0) cc_final: 0.8182 (m-30) REVERT: K 42 GLN cc_start: 0.7448 (mp10) cc_final: 0.6878 (mp10) REVERT: K 78 VAL cc_start: 0.8214 (t) cc_final: 0.7961 (t) REVERT: K 100 GLN cc_start: 0.8073 (pp30) cc_final: 0.7822 (pp30) REVERT: M 52 ASP cc_start: 0.8182 (m-30) cc_final: 0.7974 (m-30) REVERT: N 42 GLN cc_start: 0.7480 (mp10) cc_final: 0.6995 (mp10) REVERT: B 575 GLN cc_start: 0.7659 (pm20) cc_final: 0.7355 (pp30) REVERT: B 584 GLU cc_start: 0.9248 (tp30) cc_final: 0.9016 (tp30) REVERT: B 590 GLN cc_start: 0.8947 (tp40) cc_final: 0.7951 (tm-30) REVERT: B 591 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8803 (tm-30) REVERT: B 650 GLN cc_start: 0.6591 (tp40) cc_final: 0.5980 (tp40) REVERT: B 655 LYS cc_start: 0.8705 (tppt) cc_final: 0.8219 (tppt) REVERT: B 658 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 590 GLN cc_start: 0.9073 (tp40) cc_final: 0.8226 (tm-30) REVERT: C 591 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8803 (tt0) REVERT: C 643 TYR cc_start: 0.9307 (m-10) cc_final: 0.8918 (m-80) REVERT: C 650 GLN cc_start: 0.6575 (tp40) cc_final: 0.6327 (tp40) REVERT: C 655 LYS cc_start: 0.8886 (tppt) cc_final: 0.8453 (tppt) REVERT: C 658 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 82 GLN cc_start: 0.7757 (mt0) cc_final: 0.7378 (pm20) REVERT: F 321 ASP cc_start: 0.7767 (t0) cc_final: 0.7425 (t0) REVERT: G 82 GLN cc_start: 0.7666 (mt0) cc_final: 0.7221 (pm20) REVERT: G 95 MET cc_start: 0.9150 (ptm) cc_final: 0.8470 (ppp) REVERT: G 104 MET cc_start: 0.8905 (tpp) cc_final: 0.8049 (tpp) REVERT: G 161 MET cc_start: 0.9132 (tpp) cc_final: 0.8809 (tpp) REVERT: G 180 ASP cc_start: 0.9200 (m-30) cc_final: 0.8903 (m-30) REVERT: G 275 GLU cc_start: 0.8593 (tt0) cc_final: 0.8357 (tm-30) REVERT: G 377 ASN cc_start: 0.9080 (t0) cc_final: 0.8669 (t0) REVERT: A 590 GLN cc_start: 0.8980 (tp40) cc_final: 0.8244 (tm-30) REVERT: A 595 ILE cc_start: 0.9369 (mm) cc_final: 0.9129 (mm) REVERT: A 607 ASN cc_start: 0.8683 (m-40) cc_final: 0.8363 (m-40) REVERT: A 650 GLN cc_start: 0.7354 (tp40) cc_final: 0.6613 (tp40) REVERT: A 658 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8005 (tm-30) REVERT: E 97 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8878 (tppt) REVERT: E 122 LEU cc_start: 0.9503 (mt) cc_final: 0.8909 (pp) REVERT: E 180 ASP cc_start: 0.9017 (m-30) cc_final: 0.8796 (m-30) REVERT: E 275 GLU cc_start: 0.8508 (tt0) cc_final: 0.8278 (tm-30) REVERT: E 321 ASP cc_start: 0.7714 (t0) cc_final: 0.7508 (t0) REVERT: E 434 MET cc_start: 0.8810 (ttp) cc_final: 0.8572 (ttp) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.1241 time to fit residues: 85.1623 Evaluate side-chains 320 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 71 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 302 ASN F 328 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 440 GLN A 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.060420 restraints weight = 67364.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062631 restraints weight = 36083.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064111 restraints weight = 23918.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065142 restraints weight = 18175.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.065791 restraints weight = 14968.625| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21297 Z= 0.184 Angle : 0.722 12.369 29217 Z= 0.340 Chirality : 0.048 0.374 3612 Planarity : 0.004 0.042 3477 Dihedral : 7.000 55.346 5349 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.65 % Favored : 93.18 % Rotamer: Outliers : 0.14 % Allowed : 0.66 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.87 (0.17), residues: 2361 helix: 1.16 (0.27), residues: 423 sheet: -0.44 (0.22), residues: 606 loop : -1.24 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 100I TYR 0.026 0.002 TYR B 643 PHE 0.020 0.002 PHE A 522 TRP 0.056 0.002 TRP B 596 HIS 0.006 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (21117) covalent geometry : angle 0.66351 / 0.33 (28722) SS BOND : bond 0.00504 / 0.33 ( 45) SS BOND : angle 1.99672 / 1.28 ( 90) hydrogen bonds : bond 0.03207 / 2.19 ( 588) hydrogen bonds : angle 5.23854 / 3.58 ( 1521) link_ALPHA1-3 : bond 0.00801 / 0.46 ( 12) link_ALPHA1-3 : angle 2.06869 / 1.21 ( 36) link_ALPHA1-6 : bond 0.00243 / 0.13 ( 9) link_ALPHA1-6 : angle 1.66180 / 1.09 ( 27) link_BETA1-4 : bond 0.00331 / 0.21 ( 45) link_BETA1-4 : angle 1.45940 / 0.97 ( 135) link_NAG-ASN : bond 0.00520 / 0.36 ( 69) link_NAG-ASN : angle 2.87990 / 1.88 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.47 seconds wall clock time: 59 minutes 56.02 seconds (3596.02 seconds total)