Starting phenix.real_space_refine on Thu Mar 5 06:58:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vn0_21246/03_2026/6vn0_21246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn0_21246/03_2026/6vn0_21246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vn0_21246/03_2026/6vn0_21246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn0_21246/03_2026/6vn0_21246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vn0_21246/03_2026/6vn0_21246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn0_21246/03_2026/6vn0_21246.map" } resolution = 4.25 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= 0.003 sd= 0.051 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 126 5.16 5 C 12525 2.51 5 N 3306 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19962 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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 Time building chain proxies: 5.02, per 1000 atoms: 0.25 Number of scatterers: 19962 At special positions: 0 Unit cell: (141.11, 145.23, 119.48, 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 126 16.00 O 4005 8.00 N 3306 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.18 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.10 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 C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.18 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.10 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.02 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.09 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.18 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.10 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA X 3 " - " MAN X 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 619 " - " ASN A 295 " " NAG A 622 " - " ASN A 355 " " NAG A 629 " - " ASN A 133 " " NAG A 632 " - " ASN A 301 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 619 " - " ASN C 295 " " NAG C 622 " - " ASN C 355 " " NAG C 629 " - " ASN C 133 " " NAG C 632 " - " ASN C 301 " " NAG D 619 " - " ASN D 295 " " NAG D 622 " - " ASN D 355 " " NAG D 629 " - " ASN D 133 " " NAG D 632 " - " ASN D 301 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN C 392 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 448 " " NAG i 1 " - " ASN D 88 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 160 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 332 " " NAG p 1 " - " ASN D 386 " " NAG q 1 " - " ASN D 392 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 448 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 23.1% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 5.134A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 661 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 646 Processing helix chain 'E' and resid 648 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 646 Processing helix chain 'F' and resid 648 through 661 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.513A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.514A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.513A pdb=" N ILE D 215 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY D 250 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR D 217 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.585A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 795 hydrogen bonds defined for protein. 1980 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: 3.57 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5262 1.33 - 1.47: 6322 1.47 - 1.60: 8620 1.60 - 1.74: 13 1.74 - 1.88: 159 Bond restraints: 20376 Sorted by residual: bond pdb=" CB HIS I 32 " pdb=" CG HIS I 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" CB HIS G 32 " pdb=" CG HIS G 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CB HIS H 32 " pdb=" CG HIS H 32 " ideal model delta sigma weight residual 1.497 1.436 0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 bond pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 ... (remaining 20371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 23849 2.42 - 4.84: 3222 4.84 - 7.26: 530 7.26 - 9.68: 53 9.68 - 12.10: 3 Bond angle restraints: 27657 Sorted by residual: angle pdb=" N LEU B 520 " pdb=" CA LEU B 520 " pdb=" C LEU B 520 " ideal model delta sigma weight residual 113.50 101.40 12.10 1.23e+00 6.61e-01 9.69e+01 angle pdb=" N LEU E 520 " pdb=" CA LEU E 520 " pdb=" C LEU E 520 " ideal model delta sigma weight residual 113.50 101.42 12.08 1.23e+00 6.61e-01 9.65e+01 angle pdb=" N LEU F 520 " pdb=" CA LEU F 520 " pdb=" C LEU F 520 " ideal model delta sigma weight residual 113.50 101.45 12.05 1.23e+00 6.61e-01 9.60e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.26 -7.70 1.02e+00 9.61e-01 5.69e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.66e+01 ... (remaining 27652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 12984 22.51 - 45.01: 366 45.01 - 67.52: 87 67.52 - 90.02: 63 90.02 - 112.53: 24 Dihedral angle restraints: 13524 sinusoidal: 6747 harmonic: 6777 Sorted by residual: dihedral pdb=" CA CYS D 126 " pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.72 73.28 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS A 126 " pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.73 73.27 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS C 126 " pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.75 73.25 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 13521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2473 0.106 - 0.212: 821 0.212 - 0.319: 86 0.319 - 0.425: 1 0.425 - 0.531: 6 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.43e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.39e+01 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 3384 not shown) Planarity restraints: 3429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " 0.076 2.00e-02 2.50e+03 7.95e-02 7.90e+01 pdb=" CG ASN E 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.89e+01 pdb=" CG ASN B 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.88e+01 pdb=" CG ASN F 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " 0.095 2.00e-02 2.50e+03 ... (remaining 3426 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5065 2.80 - 3.32: 17794 3.32 - 3.85: 33633 3.85 - 4.37: 39409 4.37 - 4.90: 63111 Nonbonded interactions: 159012 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG i 1 " pdb=" O7 NAG i 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.270 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.308 3.120 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.308 3.120 ... (remaining 159007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'X' selection = chain 'b' selection = chain 'i' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.380 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.019 0.145 20520 Z= 0.985 Angle : 1.779 12.105 28050 Z= 1.123 Chirality : 0.098 0.531 3387 Planarity : 0.009 0.049 3375 Dihedral : 12.940 112.525 9045 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.65 % Allowed : 2.86 % Favored : 96.49 % Rotamer: Outliers : 0.15 % Allowed : 1.02 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2310 helix: -0.39 (0.24), residues: 390 sheet: 1.07 (0.20), residues: 630 loop : 0.58 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.060 0.009 TYR E 638 PHE 0.040 0.007 PHE E 522 TRP 0.051 0.010 TRP E 571 HIS 0.017 0.004 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.01834 (20376) covalent geometry : angle 1.76049 (27657) SS BOND : bond 0.05049 ( 39) SS BOND : angle 2.96607 ( 78) hydrogen bonds : bond 0.19258 ( 747) hydrogen bonds : angle 8.16803 ( 1980) link_ALPHA1-2 : bond 0.04085 ( 3) link_ALPHA1-2 : angle 2.35557 ( 9) link_ALPHA1-3 : bond 0.04231 ( 6) link_ALPHA1-3 : angle 3.46683 ( 18) link_ALPHA1-6 : bond 0.03315 ( 3) link_ALPHA1-6 : angle 2.36337 ( 9) link_BETA1-4 : bond 0.03475 ( 39) link_BETA1-4 : angle 3.33177 ( 117) link_NAG-ASN : bond 0.02955 ( 54) link_NAG-ASN : angle 2.16018 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 815 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8629 (mt) cc_final: 0.8171 (mm) REVERT: A 116 LEU cc_start: 0.8467 (mt) cc_final: 0.7941 (mt) REVERT: A 323 ILE cc_start: 0.8410 (mt) cc_final: 0.8158 (mt) REVERT: A 373 THR cc_start: 0.8850 (p) cc_final: 0.8397 (p) REVERT: A 450 THR cc_start: 0.8387 (p) cc_final: 0.7691 (t) REVERT: B 586 TYR cc_start: 0.9136 (t80) cc_final: 0.8540 (t80) REVERT: B 604 CYS cc_start: 0.5202 (t) cc_final: 0.4881 (t) REVERT: H 25 SER cc_start: 0.7152 (t) cc_final: 0.5123 (p) REVERT: L 10 PHE cc_start: 0.7351 (p90) cc_final: 0.7092 (p90) REVERT: L 21 ILE cc_start: 0.8754 (pt) cc_final: 0.8534 (mm) REVERT: L 92 ASN cc_start: 0.8912 (t0) cc_final: 0.8368 (t0) REVERT: C 52 LEU cc_start: 0.8588 (mt) cc_final: 0.8220 (mm) REVERT: C 116 LEU cc_start: 0.8643 (mt) cc_final: 0.8263 (mt) REVERT: C 251 ILE cc_start: 0.9410 (mt) cc_final: 0.9198 (tp) REVERT: C 373 THR cc_start: 0.8858 (p) cc_final: 0.8398 (p) REVERT: C 450 THR cc_start: 0.8362 (p) cc_final: 0.7676 (t) REVERT: E 584 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8502 (mt-10) REVERT: E 610 TRP cc_start: 0.8569 (t-100) cc_final: 0.8155 (t-100) REVERT: G 25 SER cc_start: 0.7059 (t) cc_final: 0.5144 (p) REVERT: J 10 PHE cc_start: 0.7430 (p90) cc_final: 0.7156 (p90) REVERT: J 21 ILE cc_start: 0.8875 (pt) cc_final: 0.8666 (mm) REVERT: J 92 ASN cc_start: 0.8877 (t0) cc_final: 0.8672 (t0) REVERT: D 52 LEU cc_start: 0.8583 (mt) cc_final: 0.8131 (mm) REVERT: D 107 ASP cc_start: 0.8614 (m-30) cc_final: 0.8386 (p0) REVERT: D 114 GLN cc_start: 0.8831 (tp40) cc_final: 0.8606 (tm-30) REVERT: D 217 TYR cc_start: 0.8344 (m-80) cc_final: 0.7409 (m-80) REVERT: D 373 THR cc_start: 0.8822 (p) cc_final: 0.8572 (p) REVERT: D 450 THR cc_start: 0.8213 (p) cc_final: 0.7537 (t) REVERT: F 543 ASN cc_start: 0.8871 (m-40) cc_final: 0.8593 (t0) REVERT: F 584 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8249 (mt-10) REVERT: I 25 SER cc_start: 0.6930 (t) cc_final: 0.4812 (p) REVERT: K 10 PHE cc_start: 0.7492 (p90) cc_final: 0.7260 (p90) REVERT: K 21 ILE cc_start: 0.8866 (pt) cc_final: 0.8636 (mm) REVERT: K 92 ASN cc_start: 0.8832 (t0) cc_final: 0.8576 (t0) outliers start: 3 outliers final: 3 residues processed: 818 average time/residue: 0.1471 time to fit residues: 182.5551 Evaluate side-chains 435 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN H 32 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 76 ASN E 550 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 35 HIS G 39 GLN J 76 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS I 39 GLN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061216 restraints weight = 72212.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063711 restraints weight = 39210.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065488 restraints weight = 25466.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066761 restraints weight = 18456.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067676 restraints weight = 14450.458| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20520 Z= 0.188 Angle : 0.881 11.377 28050 Z= 0.433 Chirality : 0.050 0.356 3387 Planarity : 0.005 0.038 3375 Dihedral : 8.705 63.539 4689 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.59 % Favored : 95.89 % Rotamer: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.50 (0.17), residues: 2310 helix: 0.56 (0.27), residues: 390 sheet: 1.01 (0.19), residues: 654 loop : -0.03 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 166 TYR 0.026 0.002 TYR I 100I PHE 0.034 0.003 PHE K 71 TRP 0.023 0.002 TRP B 610 HIS 0.010 0.002 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00421 (20376) covalent geometry : angle 0.82723 (27657) SS BOND : bond 0.00655 ( 39) SS BOND : angle 1.14628 ( 78) hydrogen bonds : bond 0.06122 ( 747) hydrogen bonds : angle 6.29441 ( 1980) link_ALPHA1-2 : bond 0.00758 ( 3) link_ALPHA1-2 : angle 1.58559 ( 9) link_ALPHA1-3 : bond 0.00866 ( 6) link_ALPHA1-3 : angle 2.03531 ( 18) link_ALPHA1-6 : bond 0.00591 ( 3) link_ALPHA1-6 : angle 1.51226 ( 9) link_BETA1-4 : bond 0.00494 ( 39) link_BETA1-4 : angle 2.57405 ( 117) link_NAG-ASN : bond 0.00717 ( 54) link_NAG-ASN : angle 3.38219 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 587 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 136 ASN cc_start: 0.8586 (m-40) cc_final: 0.8185 (m110) REVERT: A 217 TYR cc_start: 0.7650 (m-80) cc_final: 0.7189 (m-80) REVERT: A 256 SER cc_start: 0.8518 (p) cc_final: 0.8036 (p) REVERT: A 373 THR cc_start: 0.8725 (p) cc_final: 0.8437 (t) REVERT: B 543 ASN cc_start: 0.9289 (t0) cc_final: 0.8903 (t0) REVERT: B 586 TYR cc_start: 0.8887 (t80) cc_final: 0.8444 (t80) REVERT: B 606 THR cc_start: 0.8714 (p) cc_final: 0.8453 (p) REVERT: B 626 MET cc_start: 0.9124 (mmp) cc_final: 0.8816 (mmm) REVERT: B 653 GLN cc_start: 0.9150 (tt0) cc_final: 0.8902 (mp10) REVERT: H 18 LEU cc_start: 0.7799 (tt) cc_final: 0.7040 (tt) REVERT: H 61 ASP cc_start: 0.9193 (p0) cc_final: 0.8967 (p0) REVERT: H 100 TYR cc_start: 0.8027 (t80) cc_final: 0.7813 (t80) REVERT: L 8 PRO cc_start: 0.3812 (Cg_endo) cc_final: 0.3534 (Cg_exo) REVERT: L 21 ILE cc_start: 0.9476 (pt) cc_final: 0.9221 (mm) REVERT: L 37 GLN cc_start: 0.8927 (pp30) cc_final: 0.8515 (pp30) REVERT: L 53 GLN cc_start: 0.8693 (tp40) cc_final: 0.8434 (tp-100) REVERT: L 82 ASP cc_start: 0.8060 (m-30) cc_final: 0.7840 (m-30) REVERT: C 211 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 217 TYR cc_start: 0.7628 (m-10) cc_final: 0.7379 (m-10) REVERT: C 373 THR cc_start: 0.8832 (p) cc_final: 0.8522 (t) REVERT: C 387 THR cc_start: 0.9523 (p) cc_final: 0.9232 (t) REVERT: C 435 TYR cc_start: 0.7985 (t80) cc_final: 0.7720 (t80) REVERT: E 529 THR cc_start: 0.8970 (p) cc_final: 0.8735 (t) REVERT: E 543 ASN cc_start: 0.9248 (t0) cc_final: 0.8847 (t0) REVERT: E 545 LEU cc_start: 0.8815 (tp) cc_final: 0.8489 (tt) REVERT: E 588 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8929 (ttp80) REVERT: E 591 GLN cc_start: 0.9454 (tp40) cc_final: 0.9002 (tp40) REVERT: E 593 LEU cc_start: 0.9609 (mt) cc_final: 0.9390 (tp) REVERT: E 626 MET cc_start: 0.9122 (mmp) cc_final: 0.8697 (mmm) REVERT: G 18 LEU cc_start: 0.7666 (tt) cc_final: 0.6833 (tt) REVERT: G 20 LEU cc_start: 0.9191 (mt) cc_final: 0.8817 (mp) REVERT: G 61 ASP cc_start: 0.9061 (p0) cc_final: 0.8707 (p0) REVERT: J 8 PRO cc_start: 0.3890 (Cg_endo) cc_final: 0.3676 (Cg_exo) REVERT: J 21 ILE cc_start: 0.9513 (pt) cc_final: 0.9193 (mm) REVERT: J 37 GLN cc_start: 0.9027 (pp30) cc_final: 0.8814 (pp30) REVERT: J 53 GLN cc_start: 0.8753 (tp40) cc_final: 0.8520 (tp-100) REVERT: J 73 LEU cc_start: 0.9343 (tp) cc_final: 0.9054 (tp) REVERT: J 82 ASP cc_start: 0.7953 (m-30) cc_final: 0.7671 (m-30) REVERT: D 52 LEU cc_start: 0.8450 (mt) cc_final: 0.8217 (mm) REVERT: D 107 ASP cc_start: 0.9146 (m-30) cc_final: 0.8755 (p0) REVERT: D 114 GLN cc_start: 0.9362 (tp40) cc_final: 0.8878 (tm-30) REVERT: D 116 LEU cc_start: 0.8536 (mt) cc_final: 0.8246 (mt) REVERT: D 256 SER cc_start: 0.7523 (t) cc_final: 0.7215 (t) REVERT: D 323 ILE cc_start: 0.8233 (mt) cc_final: 0.7973 (tt) REVERT: D 373 THR cc_start: 0.8787 (p) cc_final: 0.8416 (t) REVERT: D 435 TYR cc_start: 0.8181 (t80) cc_final: 0.7832 (t80) REVERT: F 529 THR cc_start: 0.8952 (p) cc_final: 0.8483 (t) REVERT: F 606 THR cc_start: 0.8767 (p) cc_final: 0.8482 (p) REVERT: F 626 MET cc_start: 0.9154 (mmp) cc_final: 0.8591 (mmm) REVERT: I 18 LEU cc_start: 0.7962 (tt) cc_final: 0.7035 (tt) REVERT: I 34 MET cc_start: 0.8876 (mmm) cc_final: 0.8573 (mmp) REVERT: I 61 ASP cc_start: 0.8987 (p0) cc_final: 0.8705 (p0) REVERT: K 8 PRO cc_start: 0.3888 (Cg_endo) cc_final: 0.3592 (Cg_exo) REVERT: K 21 ILE cc_start: 0.9520 (pt) cc_final: 0.9293 (mm) REVERT: K 33 LEU cc_start: 0.8554 (tp) cc_final: 0.7943 (tp) REVERT: K 53 GLN cc_start: 0.8845 (tp40) cc_final: 0.8616 (tp-100) REVERT: K 78 LEU cc_start: 0.9253 (tp) cc_final: 0.8928 (tp) outliers start: 1 outliers final: 0 residues processed: 587 average time/residue: 0.1274 time to fit residues: 119.8782 Evaluate side-chains 440 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 10 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 222 optimal weight: 0.9990 chunk 188 optimal weight: 0.4980 chunk 176 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS C 72 HIS E 550 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS J 6 GLN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060220 restraints weight = 75937.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062624 restraints weight = 41681.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064311 restraints weight = 27268.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065528 restraints weight = 19916.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066413 restraints weight = 15624.792| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20520 Z= 0.154 Angle : 0.762 13.348 28050 Z= 0.371 Chirality : 0.047 0.304 3387 Planarity : 0.004 0.076 3375 Dihedral : 7.013 51.085 4689 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.24 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.38 (0.17), residues: 2310 helix: 0.47 (0.27), residues: 408 sheet: 0.99 (0.19), residues: 639 loop : -0.15 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 585 TYR 0.030 0.001 TYR C 217 PHE 0.022 0.002 PHE D 53 TRP 0.014 0.002 TRP F 596 HIS 0.008 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00341 (20376) covalent geometry : angle 0.71543 (27657) SS BOND : bond 0.00400 ( 39) SS BOND : angle 1.04321 ( 78) hydrogen bonds : bond 0.04948 ( 747) hydrogen bonds : angle 5.90668 ( 1980) link_ALPHA1-2 : bond 0.00614 ( 3) link_ALPHA1-2 : angle 1.66520 ( 9) link_ALPHA1-3 : bond 0.01061 ( 6) link_ALPHA1-3 : angle 1.08899 ( 18) link_ALPHA1-6 : bond 0.00803 ( 3) link_ALPHA1-6 : angle 1.75801 ( 9) link_BETA1-4 : bond 0.00458 ( 39) link_BETA1-4 : angle 2.02824 ( 117) link_NAG-ASN : bond 0.00508 ( 54) link_NAG-ASN : angle 3.03198 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8596 (m-40) cc_final: 0.8240 (m110) REVERT: A 211 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 256 SER cc_start: 0.8281 (p) cc_final: 0.7861 (p) REVERT: B 529 THR cc_start: 0.8987 (p) cc_final: 0.8622 (t) REVERT: B 543 ASN cc_start: 0.9174 (t0) cc_final: 0.8788 (t0) REVERT: B 586 TYR cc_start: 0.8868 (t80) cc_final: 0.8523 (t80) REVERT: B 593 LEU cc_start: 0.9697 (tp) cc_final: 0.9421 (tp) REVERT: B 626 MET cc_start: 0.9207 (mmp) cc_final: 0.8797 (mmm) REVERT: H 18 LEU cc_start: 0.8120 (tt) cc_final: 0.7638 (tt) REVERT: H 27 PHE cc_start: 0.7465 (p90) cc_final: 0.6997 (p90) REVERT: H 100 TYR cc_start: 0.8266 (t80) cc_final: 0.8051 (t80) REVERT: L 8 PRO cc_start: 0.4288 (Cg_endo) cc_final: 0.4072 (Cg_exo) REVERT: L 33 LEU cc_start: 0.8560 (tp) cc_final: 0.8115 (tp) REVERT: L 37 GLN cc_start: 0.8870 (pp30) cc_final: 0.8617 (pp30) REVERT: L 47 LEU cc_start: 0.9602 (mm) cc_final: 0.9339 (mm) REVERT: L 55 ILE cc_start: 0.8809 (mt) cc_final: 0.8543 (pt) REVERT: C 67 ASN cc_start: 0.8591 (p0) cc_final: 0.8387 (p0) REVERT: C 116 LEU cc_start: 0.8565 (mt) cc_final: 0.8334 (mt) REVERT: C 136 ASN cc_start: 0.8507 (m-40) cc_final: 0.8159 (m110) REVERT: C 161 MET cc_start: 0.9059 (tpt) cc_final: 0.8799 (tmm) REVERT: C 256 SER cc_start: 0.8350 (m) cc_final: 0.8121 (m) REVERT: C 435 TYR cc_start: 0.8195 (t80) cc_final: 0.7704 (t80) REVERT: C 454 LEU cc_start: 0.9652 (mp) cc_final: 0.9391 (mt) REVERT: E 543 ASN cc_start: 0.9156 (t0) cc_final: 0.8869 (t0) REVERT: E 545 LEU cc_start: 0.8855 (tp) cc_final: 0.8466 (tt) REVERT: E 591 GLN cc_start: 0.9508 (tp40) cc_final: 0.8995 (tp40) REVERT: E 632 ASP cc_start: 0.9253 (t70) cc_final: 0.8973 (t70) REVERT: G 18 LEU cc_start: 0.7951 (tt) cc_final: 0.7205 (tt) REVERT: G 20 LEU cc_start: 0.9324 (mt) cc_final: 0.8992 (mp) REVERT: G 61 ASP cc_start: 0.9064 (p0) cc_final: 0.8774 (p0) REVERT: J 53 GLN cc_start: 0.8851 (tp40) cc_final: 0.8588 (tp-100) REVERT: J 71 PHE cc_start: 0.8926 (m-10) cc_final: 0.8678 (m-10) REVERT: D 104 MET cc_start: 0.9596 (ttm) cc_final: 0.9112 (ttm) REVERT: D 107 ASP cc_start: 0.9063 (m-30) cc_final: 0.8823 (p0) REVERT: D 114 GLN cc_start: 0.9322 (tp40) cc_final: 0.8938 (tm-30) REVERT: D 116 LEU cc_start: 0.8768 (mt) cc_final: 0.8525 (mt) REVERT: D 136 ASN cc_start: 0.8442 (m-40) cc_final: 0.8030 (m110) REVERT: D 211 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7185 (tm-30) REVERT: D 256 SER cc_start: 0.7667 (t) cc_final: 0.7367 (t) REVERT: D 435 TYR cc_start: 0.8108 (t80) cc_final: 0.7678 (t80) REVERT: D 454 LEU cc_start: 0.9573 (mp) cc_final: 0.9368 (mt) REVERT: F 539 VAL cc_start: 0.9828 (t) cc_final: 0.9601 (p) REVERT: F 543 ASN cc_start: 0.9193 (t0) cc_final: 0.8874 (t0) REVERT: F 603 ILE cc_start: 0.8880 (mm) cc_final: 0.8660 (mm) REVERT: F 621 GLU cc_start: 0.8394 (tp30) cc_final: 0.7775 (tp30) REVERT: I 18 LEU cc_start: 0.7843 (tt) cc_final: 0.7303 (tt) REVERT: I 34 MET cc_start: 0.8900 (mmm) cc_final: 0.8600 (mmm) REVERT: I 47 TRP cc_start: 0.8612 (t60) cc_final: 0.8313 (t60) REVERT: I 58 TYR cc_start: 0.9229 (m-80) cc_final: 0.8945 (m-10) REVERT: I 100 TYR cc_start: 0.8041 (t80) cc_final: 0.7773 (t80) REVERT: K 37 GLN cc_start: 0.8988 (pp30) cc_final: 0.8736 (pp30) REVERT: K 78 LEU cc_start: 0.9231 (tp) cc_final: 0.8953 (tp) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.1187 time to fit residues: 101.9524 Evaluate side-chains 400 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 175 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.054458 restraints weight = 80484.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.056541 restraints weight = 44722.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.058031 restraints weight = 29829.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059059 restraints weight = 22160.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059854 restraints weight = 17843.803| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 20520 Z= 0.247 Angle : 0.846 13.489 28050 Z= 0.413 Chirality : 0.048 0.259 3387 Planarity : 0.005 0.063 3375 Dihedral : 6.489 56.331 4689 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.89 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.00 (0.17), residues: 2310 helix: 0.56 (0.26), residues: 393 sheet: 0.58 (0.19), residues: 678 loop : -0.46 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 617 TYR 0.025 0.002 TYR I 100A PHE 0.036 0.003 PHE A 53 TRP 0.032 0.003 TRP G 100H HIS 0.006 0.002 HIS I 54 Details of bonding type rmsd covalent geometry : bond 0.00542 (20376) covalent geometry : angle 0.80372 (27657) SS BOND : bond 0.00635 ( 39) SS BOND : angle 1.33822 ( 78) hydrogen bonds : bond 0.05101 ( 747) hydrogen bonds : angle 5.82832 ( 1980) link_ALPHA1-2 : bond 0.00379 ( 3) link_ALPHA1-2 : angle 1.63073 ( 9) link_ALPHA1-3 : bond 0.01020 ( 6) link_ALPHA1-3 : angle 1.05274 ( 18) link_ALPHA1-6 : bond 0.00287 ( 3) link_ALPHA1-6 : angle 1.50975 ( 9) link_BETA1-4 : bond 0.00311 ( 39) link_BETA1-4 : angle 1.91003 ( 117) link_NAG-ASN : bond 0.00535 ( 54) link_NAG-ASN : angle 3.09989 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 0.724 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: A 95 MET cc_start: 0.9324 (pmm) cc_final: 0.8958 (pmm) REVERT: A 116 LEU cc_start: 0.8842 (mt) cc_final: 0.8445 (mt) REVERT: A 136 ASN cc_start: 0.8598 (m-40) cc_final: 0.8261 (m110) REVERT: A 435 TYR cc_start: 0.8696 (t80) cc_final: 0.8449 (t80) REVERT: B 530 MET cc_start: 0.9311 (mmm) cc_final: 0.9053 (mmm) REVERT: B 543 ASN cc_start: 0.9216 (t0) cc_final: 0.8868 (t0) REVERT: B 626 MET cc_start: 0.9115 (mmp) cc_final: 0.8812 (mmm) REVERT: H 100 TYR cc_start: 0.8633 (t80) cc_final: 0.8348 (t80) REVERT: L 37 GLN cc_start: 0.8866 (pp30) cc_final: 0.8632 (pp30) REVERT: L 55 ILE cc_start: 0.8948 (mt) cc_final: 0.8730 (pt) REVERT: L 71 PHE cc_start: 0.8982 (m-80) cc_final: 0.8657 (m-80) REVERT: L 92 ASN cc_start: 0.9118 (t0) cc_final: 0.8911 (t0) REVERT: C 53 PHE cc_start: 0.5525 (m-80) cc_final: 0.5295 (m-80) REVERT: C 67 ASN cc_start: 0.8890 (p0) cc_final: 0.8550 (p0) REVERT: C 95 MET cc_start: 0.9298 (pmm) cc_final: 0.8890 (pmm) REVERT: C 116 LEU cc_start: 0.8648 (mt) cc_final: 0.7563 (mt) REVERT: C 136 ASN cc_start: 0.8665 (m-40) cc_final: 0.8380 (m110) REVERT: C 435 TYR cc_start: 0.8487 (t80) cc_final: 0.7895 (t80) REVERT: E 543 ASN cc_start: 0.9150 (t0) cc_final: 0.8858 (t0) REVERT: E 545 LEU cc_start: 0.8978 (tp) cc_final: 0.8457 (tt) REVERT: E 591 GLN cc_start: 0.9502 (tp40) cc_final: 0.9124 (tp40) REVERT: E 632 ASP cc_start: 0.9360 (t70) cc_final: 0.9118 (t70) REVERT: G 20 LEU cc_start: 0.9473 (mt) cc_final: 0.9225 (mp) REVERT: G 26 GLU cc_start: 0.7984 (mp0) cc_final: 0.7738 (mp0) REVERT: G 35 HIS cc_start: 0.9155 (m90) cc_final: 0.8724 (m90) REVERT: G 78 LEU cc_start: 0.9042 (mt) cc_final: 0.8784 (mt) REVERT: G 107 THR cc_start: 0.8993 (m) cc_final: 0.8769 (p) REVERT: J 71 PHE cc_start: 0.9020 (m-80) cc_final: 0.8770 (m-10) REVERT: D 95 MET cc_start: 0.9238 (pmm) cc_final: 0.8904 (pmm) REVERT: D 104 MET cc_start: 0.9678 (ttm) cc_final: 0.9468 (ttm) REVERT: D 107 ASP cc_start: 0.9086 (m-30) cc_final: 0.8680 (m-30) REVERT: D 116 LEU cc_start: 0.8818 (mt) cc_final: 0.8205 (mt) REVERT: D 136 ASN cc_start: 0.8477 (m-40) cc_final: 0.8098 (m110) REVERT: D 173 TYR cc_start: 0.8359 (p90) cc_final: 0.7847 (p90) REVERT: D 246 GLN cc_start: 0.7568 (pm20) cc_final: 0.7270 (pm20) REVERT: D 260 LEU cc_start: 0.9260 (mt) cc_final: 0.8844 (mp) REVERT: D 271 MET cc_start: 0.9132 (mmp) cc_final: 0.8920 (mmm) REVERT: D 426 MET cc_start: 0.9267 (ttm) cc_final: 0.9041 (ttp) REVERT: D 435 TYR cc_start: 0.8411 (t80) cc_final: 0.7931 (t80) REVERT: F 543 ASN cc_start: 0.9143 (t0) cc_final: 0.8847 (t0) REVERT: F 591 GLN cc_start: 0.9466 (tp40) cc_final: 0.8972 (tp40) REVERT: F 621 GLU cc_start: 0.8282 (tp30) cc_final: 0.7915 (tp30) REVERT: F 626 MET cc_start: 0.9091 (mmp) cc_final: 0.8826 (mmm) REVERT: I 34 MET cc_start: 0.8837 (mmm) cc_final: 0.8568 (mmm) REVERT: I 100 TYR cc_start: 0.8488 (t80) cc_final: 0.8236 (t80) REVERT: K 21 ILE cc_start: 0.9478 (pt) cc_final: 0.9165 (mm) REVERT: K 37 GLN cc_start: 0.8969 (pp30) cc_final: 0.8693 (pp30) REVERT: K 87 TYR cc_start: 0.9090 (m-80) cc_final: 0.8579 (m-10) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.1161 time to fit residues: 92.2688 Evaluate side-chains 368 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 226 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.054556 restraints weight = 79490.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056659 restraints weight = 43914.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058120 restraints weight = 29096.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059195 restraints weight = 21638.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059967 restraints weight = 17297.246| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20520 Z= 0.189 Angle : 0.751 13.164 28050 Z= 0.366 Chirality : 0.046 0.257 3387 Planarity : 0.004 0.057 3375 Dihedral : 6.271 59.499 4689 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.58 % Favored : 94.11 % Rotamer: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.09 (0.17), residues: 2310 helix: 0.45 (0.26), residues: 414 sheet: 0.63 (0.19), residues: 669 loop : -0.59 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 151 TYR 0.015 0.001 TYR L 50 PHE 0.028 0.002 PHE A 53 TRP 0.023 0.002 TRP E 628 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00427 (20376) covalent geometry : angle 0.70965 (27657) SS BOND : bond 0.00443 ( 39) SS BOND : angle 1.23081 ( 78) hydrogen bonds : bond 0.04528 ( 747) hydrogen bonds : angle 5.72119 ( 1980) link_ALPHA1-2 : bond 0.00399 ( 3) link_ALPHA1-2 : angle 1.71225 ( 9) link_ALPHA1-3 : bond 0.01114 ( 6) link_ALPHA1-3 : angle 1.13738 ( 18) link_ALPHA1-6 : bond 0.00265 ( 3) link_ALPHA1-6 : angle 1.53079 ( 9) link_BETA1-4 : bond 0.00356 ( 39) link_BETA1-4 : angle 1.75057 ( 117) link_NAG-ASN : bond 0.00415 ( 54) link_NAG-ASN : angle 2.88921 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 0.620 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: A 67 ASN cc_start: 0.8738 (m-40) cc_final: 0.8436 (p0) REVERT: A 95 MET cc_start: 0.9191 (pmm) cc_final: 0.8796 (pmm) REVERT: A 98 ASN cc_start: 0.9272 (t0) cc_final: 0.8906 (t0) REVERT: A 116 LEU cc_start: 0.8829 (mt) cc_final: 0.8178 (mt) REVERT: A 136 ASN cc_start: 0.8594 (m-40) cc_final: 0.8261 (m110) REVERT: A 256 SER cc_start: 0.8471 (p) cc_final: 0.8113 (t) REVERT: A 435 TYR cc_start: 0.8661 (t80) cc_final: 0.8417 (t80) REVERT: B 543 ASN cc_start: 0.9102 (t0) cc_final: 0.8788 (t0) REVERT: B 626 MET cc_start: 0.9168 (mmp) cc_final: 0.8799 (mmm) REVERT: L 18 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8901 (mptt) REVERT: L 53 GLN cc_start: 0.9014 (tp40) cc_final: 0.8781 (tp-100) REVERT: L 92 ASN cc_start: 0.9296 (t0) cc_final: 0.8944 (t0) REVERT: C 67 ASN cc_start: 0.8954 (p0) cc_final: 0.8657 (p0) REVERT: C 95 MET cc_start: 0.9176 (pmm) cc_final: 0.8883 (pmm) REVERT: C 136 ASN cc_start: 0.8677 (m-40) cc_final: 0.8389 (m110) REVERT: C 256 SER cc_start: 0.8407 (m) cc_final: 0.8173 (m) REVERT: C 435 TYR cc_start: 0.8633 (t80) cc_final: 0.8060 (t80) REVERT: E 543 ASN cc_start: 0.9150 (t0) cc_final: 0.8873 (t0) REVERT: E 548 ILE cc_start: 0.8566 (tp) cc_final: 0.8117 (pt) REVERT: E 584 GLU cc_start: 0.9242 (tt0) cc_final: 0.9018 (tt0) REVERT: E 591 GLN cc_start: 0.9524 (tp40) cc_final: 0.9043 (tp40) REVERT: E 626 MET cc_start: 0.9177 (mmp) cc_final: 0.8850 (mmm) REVERT: E 632 ASP cc_start: 0.9345 (t70) cc_final: 0.9057 (t70) REVERT: G 33 ASP cc_start: 0.8124 (p0) cc_final: 0.7394 (p0) REVERT: G 61 ASP cc_start: 0.9089 (p0) cc_final: 0.8591 (t0) REVERT: G 107 THR cc_start: 0.9065 (m) cc_final: 0.8777 (p) REVERT: J 37 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8872 (pp30) REVERT: J 55 ILE cc_start: 0.9345 (pt) cc_final: 0.9064 (pt) REVERT: J 71 PHE cc_start: 0.9172 (m-80) cc_final: 0.8822 (m-10) REVERT: J 73 LEU cc_start: 0.9523 (pt) cc_final: 0.9316 (pt) REVERT: D 95 MET cc_start: 0.9139 (pmm) cc_final: 0.8864 (pmm) REVERT: D 98 ASN cc_start: 0.9368 (t0) cc_final: 0.9016 (t0) REVERT: D 104 MET cc_start: 0.9621 (ttm) cc_final: 0.9416 (ttm) REVERT: D 173 TYR cc_start: 0.8388 (p90) cc_final: 0.7853 (p90) REVERT: D 435 TYR cc_start: 0.8423 (t80) cc_final: 0.7800 (t80) REVERT: F 530 MET cc_start: 0.9255 (mmm) cc_final: 0.8944 (mmm) REVERT: F 543 ASN cc_start: 0.9151 (t0) cc_final: 0.8946 (t0) REVERT: F 598 CYS cc_start: 0.6822 (m) cc_final: 0.6352 (m) REVERT: F 621 GLU cc_start: 0.8279 (tp30) cc_final: 0.7980 (tp30) REVERT: F 626 MET cc_start: 0.9053 (mmp) cc_final: 0.8838 (mmm) REVERT: I 34 MET cc_start: 0.8882 (mmm) cc_final: 0.8613 (mmm) REVERT: I 61 ASP cc_start: 0.9014 (p0) cc_final: 0.8425 (t0) REVERT: I 100 TYR cc_start: 0.8512 (t80) cc_final: 0.8306 (t80) REVERT: K 37 GLN cc_start: 0.8917 (pp30) cc_final: 0.8699 (pp30) REVERT: K 53 GLN cc_start: 0.9100 (tp40) cc_final: 0.8899 (tp-100) REVERT: K 87 TYR cc_start: 0.9116 (m-80) cc_final: 0.8892 (m-80) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.1150 time to fit residues: 86.8136 Evaluate side-chains 356 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 143 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 221 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053578 restraints weight = 78717.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055681 restraints weight = 43171.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.057167 restraints weight = 28478.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058221 restraints weight = 21027.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058984 restraints weight = 16805.226| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20520 Z= 0.182 Angle : 0.756 13.070 28050 Z= 0.369 Chirality : 0.047 0.250 3387 Planarity : 0.004 0.060 3375 Dihedral : 6.139 56.420 4689 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.45 % Favored : 93.29 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.29 (0.18), residues: 2310 helix: 0.36 (0.26), residues: 420 sheet: 0.26 (0.18), residues: 738 loop : -0.64 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 66 TYR 0.018 0.002 TYR H 100A PHE 0.027 0.003 PHE I 91 TRP 0.018 0.002 TRP C 69 HIS 0.008 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00410 (20376) covalent geometry : angle 0.71648 (27657) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.18460 ( 78) hydrogen bonds : bond 0.04565 ( 747) hydrogen bonds : angle 5.77076 ( 1980) link_ALPHA1-2 : bond 0.00366 ( 3) link_ALPHA1-2 : angle 1.72079 ( 9) link_ALPHA1-3 : bond 0.01032 ( 6) link_ALPHA1-3 : angle 1.17359 ( 18) link_ALPHA1-6 : bond 0.00304 ( 3) link_ALPHA1-6 : angle 1.51534 ( 9) link_BETA1-4 : bond 0.00324 ( 39) link_BETA1-4 : angle 1.73157 ( 117) link_NAG-ASN : bond 0.00441 ( 54) link_NAG-ASN : angle 2.81917 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.717 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: A 67 ASN cc_start: 0.8779 (m-40) cc_final: 0.8467 (p0) REVERT: A 98 ASN cc_start: 0.9237 (t0) cc_final: 0.8940 (t0) REVERT: A 256 SER cc_start: 0.8685 (p) cc_final: 0.8214 (p) REVERT: A 435 TYR cc_start: 0.8723 (t80) cc_final: 0.8421 (t80) REVERT: B 543 ASN cc_start: 0.9213 (t0) cc_final: 0.8873 (t0) REVERT: B 626 MET cc_start: 0.9113 (mmp) cc_final: 0.8742 (mmm) REVERT: L 37 GLN cc_start: 0.9000 (pp30) cc_final: 0.8515 (pp30) REVERT: L 53 GLN cc_start: 0.9007 (tp40) cc_final: 0.8783 (tp-100) REVERT: L 55 ILE cc_start: 0.9247 (pt) cc_final: 0.8918 (pt) REVERT: L 92 ASN cc_start: 0.9254 (t0) cc_final: 0.9018 (t0) REVERT: C 67 ASN cc_start: 0.9013 (p0) cc_final: 0.8728 (p0) REVERT: C 95 MET cc_start: 0.9259 (pmm) cc_final: 0.8998 (pmm) REVERT: C 136 ASN cc_start: 0.8756 (m-40) cc_final: 0.8532 (m-40) REVERT: C 256 SER cc_start: 0.8403 (m) cc_final: 0.8147 (m) REVERT: C 435 TYR cc_start: 0.8639 (t80) cc_final: 0.7894 (t80) REVERT: C 477 ASP cc_start: 0.9209 (m-30) cc_final: 0.8892 (p0) REVERT: E 543 ASN cc_start: 0.9202 (t0) cc_final: 0.8954 (t0) REVERT: E 584 GLU cc_start: 0.9291 (tt0) cc_final: 0.9048 (tt0) REVERT: E 589 ASP cc_start: 0.9261 (m-30) cc_final: 0.8972 (m-30) REVERT: E 591 GLN cc_start: 0.9548 (tp40) cc_final: 0.9091 (tp40) REVERT: E 598 CYS cc_start: 0.6896 (m) cc_final: 0.6548 (m) REVERT: E 626 MET cc_start: 0.9127 (mmp) cc_final: 0.8866 (mmm) REVERT: E 632 ASP cc_start: 0.9395 (t70) cc_final: 0.9093 (t70) REVERT: G 33 ASP cc_start: 0.8072 (p0) cc_final: 0.7303 (p0) REVERT: G 61 ASP cc_start: 0.9121 (p0) cc_final: 0.8529 (t0) REVERT: J 71 PHE cc_start: 0.9097 (m-80) cc_final: 0.8882 (m-10) REVERT: D 95 MET cc_start: 0.9252 (pmm) cc_final: 0.8996 (pmm) REVERT: D 107 ASP cc_start: 0.9165 (m-30) cc_final: 0.8874 (m-30) REVERT: D 111 LEU cc_start: 0.9493 (tt) cc_final: 0.9221 (pp) REVERT: D 136 ASN cc_start: 0.8723 (m110) cc_final: 0.8451 (m110) REVERT: D 173 TYR cc_start: 0.8312 (p90) cc_final: 0.7863 (p90) REVERT: D 260 LEU cc_start: 0.9206 (mt) cc_final: 0.8486 (mp) REVERT: D 435 TYR cc_start: 0.8591 (t80) cc_final: 0.7827 (t80) REVERT: D 475 MET cc_start: 0.8250 (mmt) cc_final: 0.7784 (mmt) REVERT: F 543 ASN cc_start: 0.9255 (t0) cc_final: 0.8890 (t0) REVERT: F 598 CYS cc_start: 0.6941 (m) cc_final: 0.6380 (m) REVERT: F 621 GLU cc_start: 0.8246 (tp30) cc_final: 0.7882 (tp30) REVERT: F 626 MET cc_start: 0.9117 (mmp) cc_final: 0.8818 (mmm) REVERT: I 34 MET cc_start: 0.8936 (mmm) cc_final: 0.8668 (mmm) REVERT: I 61 ASP cc_start: 0.9088 (p0) cc_final: 0.8434 (t0) REVERT: I 80 LEU cc_start: 0.8931 (tp) cc_final: 0.8028 (tp) REVERT: I 100 TYR cc_start: 0.8563 (t80) cc_final: 0.8338 (t80) REVERT: K 37 GLN cc_start: 0.8957 (pp30) cc_final: 0.8745 (pp30) REVERT: K 71 PHE cc_start: 0.9002 (m-80) cc_final: 0.8415 (m-10) REVERT: K 73 LEU cc_start: 0.9518 (pt) cc_final: 0.9297 (pt) outliers start: 1 outliers final: 1 residues processed: 441 average time/residue: 0.1117 time to fit residues: 82.3431 Evaluate side-chains 354 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 151 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS L 6 GLN C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN K 6 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.054006 restraints weight = 77252.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.056185 restraints weight = 41612.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057740 restraints weight = 27265.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058838 restraints weight = 20012.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059655 restraints weight = 15919.266| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20520 Z= 0.132 Angle : 0.724 12.166 28050 Z= 0.348 Chirality : 0.049 0.548 3387 Planarity : 0.004 0.051 3375 Dihedral : 6.057 55.565 4689 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.10 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.23 (0.18), residues: 2310 helix: 0.59 (0.26), residues: 408 sheet: 0.45 (0.19), residues: 702 loop : -0.75 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.017 0.001 TYR K 87 PHE 0.022 0.002 PHE D 53 TRP 0.030 0.002 TRP A 427 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (20376) covalent geometry : angle 0.68389 (27657) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.10097 ( 78) hydrogen bonds : bond 0.04134 ( 747) hydrogen bonds : angle 5.72615 ( 1980) link_ALPHA1-2 : bond 0.00408 ( 3) link_ALPHA1-2 : angle 1.80681 ( 9) link_ALPHA1-3 : bond 0.00974 ( 6) link_ALPHA1-3 : angle 1.18676 ( 18) link_ALPHA1-6 : bond 0.00409 ( 3) link_ALPHA1-6 : angle 1.42202 ( 9) link_BETA1-4 : bond 0.00387 ( 39) link_BETA1-4 : angle 1.68467 ( 117) link_NAG-ASN : bond 0.00548 ( 54) link_NAG-ASN : angle 2.79649 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.778 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: A 67 ASN cc_start: 0.8840 (m-40) cc_final: 0.8484 (p0) REVERT: A 98 ASN cc_start: 0.9191 (t0) cc_final: 0.8880 (t0) REVERT: A 103 GLN cc_start: 0.9453 (mm110) cc_final: 0.9175 (tp40) REVERT: A 136 ASN cc_start: 0.8862 (m-40) cc_final: 0.8516 (m110) REVERT: A 256 SER cc_start: 0.8708 (p) cc_final: 0.8172 (p) REVERT: A 435 TYR cc_start: 0.8772 (t80) cc_final: 0.8422 (t80) REVERT: B 520 LEU cc_start: 0.8639 (mm) cc_final: 0.8236 (mt) REVERT: B 530 MET cc_start: 0.8808 (tpp) cc_final: 0.8556 (tpp) REVERT: B 543 ASN cc_start: 0.9246 (t0) cc_final: 0.8982 (t0) REVERT: B 593 LEU cc_start: 0.9736 (tp) cc_final: 0.9528 (tp) REVERT: B 626 MET cc_start: 0.9109 (mmp) cc_final: 0.8461 (mmm) REVERT: H 61 ASP cc_start: 0.9083 (p0) cc_final: 0.8444 (t0) REVERT: H 80 LEU cc_start: 0.8529 (tt) cc_final: 0.7554 (tp) REVERT: H 82 LEU cc_start: 0.8791 (mt) cc_final: 0.8458 (mt) REVERT: L 37 GLN cc_start: 0.9004 (pp30) cc_final: 0.8611 (pp30) REVERT: L 53 GLN cc_start: 0.9099 (tp40) cc_final: 0.8891 (tp-100) REVERT: C 67 ASN cc_start: 0.9072 (p0) cc_final: 0.8797 (p0) REVERT: C 95 MET cc_start: 0.9194 (pmm) cc_final: 0.8864 (pmm) REVERT: C 136 ASN cc_start: 0.8772 (m-40) cc_final: 0.8545 (m-40) REVERT: C 256 SER cc_start: 0.8393 (m) cc_final: 0.8123 (m) REVERT: C 427 TRP cc_start: 0.7898 (m-10) cc_final: 0.7148 (m-90) REVERT: C 435 TYR cc_start: 0.8624 (t80) cc_final: 0.7929 (t80) REVERT: C 477 ASP cc_start: 0.9205 (m-30) cc_final: 0.8860 (p0) REVERT: E 543 ASN cc_start: 0.9260 (t0) cc_final: 0.9030 (t0) REVERT: E 589 ASP cc_start: 0.9244 (m-30) cc_final: 0.8958 (m-30) REVERT: E 591 GLN cc_start: 0.9552 (tp40) cc_final: 0.9012 (tp40) REVERT: E 598 CYS cc_start: 0.6932 (m) cc_final: 0.6647 (m) REVERT: E 626 MET cc_start: 0.9002 (mmp) cc_final: 0.8767 (mmm) REVERT: G 33 ASP cc_start: 0.7928 (p0) cc_final: 0.7484 (p0) REVERT: G 35 HIS cc_start: 0.9218 (m-70) cc_final: 0.8690 (m-70) REVERT: G 61 ASP cc_start: 0.9155 (p0) cc_final: 0.8531 (t0) REVERT: J 17 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8695 (mt-10) REVERT: J 23 CYS cc_start: 0.2990 (m) cc_final: 0.2039 (m) REVERT: J 35 TRP cc_start: 0.8811 (m100) cc_final: 0.8366 (m100) REVERT: D 95 MET cc_start: 0.9216 (pmm) cc_final: 0.8952 (pmm) REVERT: D 104 MET cc_start: 0.9751 (ttt) cc_final: 0.9489 (ttt) REVERT: D 107 ASP cc_start: 0.9190 (m-30) cc_final: 0.8903 (m-30) REVERT: D 111 LEU cc_start: 0.9476 (tt) cc_final: 0.9221 (pp) REVERT: D 136 ASN cc_start: 0.8762 (m110) cc_final: 0.8478 (m110) REVERT: D 173 TYR cc_start: 0.8250 (p90) cc_final: 0.7888 (p90) REVERT: D 201 ILE cc_start: 0.9081 (mp) cc_final: 0.8843 (tp) REVERT: D 260 LEU cc_start: 0.9191 (mt) cc_final: 0.8470 (mp) REVERT: D 323 ILE cc_start: 0.9138 (mp) cc_final: 0.8794 (tt) REVERT: D 435 TYR cc_start: 0.8571 (t80) cc_final: 0.7815 (t80) REVERT: D 475 MET cc_start: 0.8202 (mmt) cc_final: 0.7722 (mmt) REVERT: F 543 ASN cc_start: 0.9263 (t0) cc_final: 0.8924 (t0) REVERT: F 626 MET cc_start: 0.9046 (mmp) cc_final: 0.8793 (mmm) REVERT: I 34 MET cc_start: 0.8925 (mmm) cc_final: 0.8628 (mmm) REVERT: I 61 ASP cc_start: 0.9060 (p0) cc_final: 0.8485 (t0) REVERT: I 80 LEU cc_start: 0.8936 (tp) cc_final: 0.8175 (tp) REVERT: I 82 MET cc_start: 0.8873 (pmm) cc_final: 0.8390 (pmm) REVERT: K 17 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8797 (mt-10) REVERT: K 18 LYS cc_start: 0.9278 (mmtt) cc_final: 0.8962 (mmmt) REVERT: K 37 GLN cc_start: 0.8868 (pp30) cc_final: 0.8646 (pp30) REVERT: K 71 PHE cc_start: 0.8939 (m-80) cc_final: 0.8484 (m-10) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.1147 time to fit residues: 88.9497 Evaluate side-chains 368 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051857 restraints weight = 80849.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053881 restraints weight = 45165.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055311 restraints weight = 30204.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056339 restraints weight = 22557.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057063 restraints weight = 18187.708| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20520 Z= 0.213 Angle : 0.783 13.478 28050 Z= 0.381 Chirality : 0.049 0.419 3387 Planarity : 0.004 0.046 3375 Dihedral : 6.251 54.983 4689 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.49 (0.17), residues: 2310 helix: 0.35 (0.26), residues: 417 sheet: 0.15 (0.18), residues: 729 loop : -0.84 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 83 TYR 0.017 0.002 TYR H 100A PHE 0.035 0.003 PHE J 71 TRP 0.037 0.002 TRP A 427 HIS 0.008 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00475 (20376) covalent geometry : angle 0.74397 (27657) SS BOND : bond 0.00422 ( 39) SS BOND : angle 1.14638 ( 78) hydrogen bonds : bond 0.04513 ( 747) hydrogen bonds : angle 5.76143 ( 1980) link_ALPHA1-2 : bond 0.00320 ( 3) link_ALPHA1-2 : angle 1.71509 ( 9) link_ALPHA1-3 : bond 0.00870 ( 6) link_ALPHA1-3 : angle 1.25286 ( 18) link_ALPHA1-6 : bond 0.00251 ( 3) link_ALPHA1-6 : angle 1.60982 ( 9) link_BETA1-4 : bond 0.00277 ( 39) link_BETA1-4 : angle 1.75478 ( 117) link_NAG-ASN : bond 0.00497 ( 54) link_NAG-ASN : angle 2.88804 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8857 (m-40) cc_final: 0.8499 (p0) REVERT: A 103 GLN cc_start: 0.9482 (mm110) cc_final: 0.9122 (tp40) REVERT: A 136 ASN cc_start: 0.8779 (m-40) cc_final: 0.8538 (m-40) REVERT: A 256 SER cc_start: 0.8661 (p) cc_final: 0.8415 (p) REVERT: A 426 MET cc_start: 0.8059 (ttt) cc_final: 0.7611 (tmm) REVERT: A 435 TYR cc_start: 0.8825 (t80) cc_final: 0.8163 (t80) REVERT: B 520 LEU cc_start: 0.8811 (mm) cc_final: 0.8410 (mt) REVERT: B 543 ASN cc_start: 0.9298 (t0) cc_final: 0.8932 (t0) REVERT: B 626 MET cc_start: 0.9085 (mmp) cc_final: 0.8554 (mmm) REVERT: H 82 MET cc_start: 0.8927 (pmm) cc_final: 0.8688 (pmm) REVERT: L 27 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8443 (tm-30) REVERT: L 37 GLN cc_start: 0.9080 (pp30) cc_final: 0.8691 (pp30) REVERT: C 67 ASN cc_start: 0.9034 (p0) cc_final: 0.8735 (p0) REVERT: C 95 MET cc_start: 0.9231 (pmm) cc_final: 0.8936 (pmm) REVERT: C 256 SER cc_start: 0.8447 (m) cc_final: 0.8187 (m) REVERT: C 435 TYR cc_start: 0.8635 (t80) cc_final: 0.7811 (t80) REVERT: C 477 ASP cc_start: 0.9189 (m-30) cc_final: 0.8893 (p0) REVERT: E 543 ASN cc_start: 0.9260 (t0) cc_final: 0.9015 (t0) REVERT: E 584 GLU cc_start: 0.9272 (tt0) cc_final: 0.9066 (tt0) REVERT: E 589 ASP cc_start: 0.9248 (m-30) cc_final: 0.8961 (m-30) REVERT: E 591 GLN cc_start: 0.9582 (tp40) cc_final: 0.9003 (tp40) REVERT: E 598 CYS cc_start: 0.7181 (m) cc_final: 0.6896 (m) REVERT: G 33 ASP cc_start: 0.8048 (p0) cc_final: 0.7390 (p0) REVERT: G 61 ASP cc_start: 0.9158 (p0) cc_final: 0.8433 (t0) REVERT: J 37 GLN cc_start: 0.9084 (pp30) cc_final: 0.8699 (pp30) REVERT: J 53 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8614 (tp-100) REVERT: D 95 MET cc_start: 0.9198 (pmm) cc_final: 0.8723 (pmm) REVERT: D 104 MET cc_start: 0.9767 (ttt) cc_final: 0.9479 (ttt) REVERT: D 107 ASP cc_start: 0.9265 (m-30) cc_final: 0.9007 (m-30) REVERT: D 111 LEU cc_start: 0.9525 (tt) cc_final: 0.9298 (pp) REVERT: D 136 ASN cc_start: 0.8749 (m110) cc_final: 0.8548 (m110) REVERT: D 173 TYR cc_start: 0.8223 (p90) cc_final: 0.7892 (p90) REVERT: D 260 LEU cc_start: 0.9197 (mt) cc_final: 0.8502 (mp) REVERT: D 435 TYR cc_start: 0.8576 (t80) cc_final: 0.7999 (t80) REVERT: D 475 MET cc_start: 0.8241 (mmt) cc_final: 0.7970 (mmt) REVERT: F 520 LEU cc_start: 0.8776 (mm) cc_final: 0.8214 (mt) REVERT: F 530 MET cc_start: 0.9224 (tpp) cc_final: 0.8427 (tpp) REVERT: F 543 ASN cc_start: 0.9286 (t0) cc_final: 0.8830 (t0) REVERT: F 621 GLU cc_start: 0.8317 (tp30) cc_final: 0.7743 (tp30) REVERT: F 626 MET cc_start: 0.9286 (mmp) cc_final: 0.8793 (mmm) REVERT: F 653 GLN cc_start: 0.8832 (mp10) cc_final: 0.8614 (mp10) REVERT: I 34 MET cc_start: 0.8967 (mmm) cc_final: 0.8714 (mmm) REVERT: I 61 ASP cc_start: 0.9089 (p0) cc_final: 0.8424 (t0) REVERT: I 80 LEU cc_start: 0.9013 (tp) cc_final: 0.8167 (tp) REVERT: I 82 MET cc_start: 0.8710 (pmm) cc_final: 0.8285 (pmm) REVERT: K 17 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8881 (mt-10) REVERT: K 37 GLN cc_start: 0.8886 (pp30) cc_final: 0.8671 (pp30) REVERT: K 53 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8603 (tp-100) REVERT: K 71 PHE cc_start: 0.8999 (m-80) cc_final: 0.8618 (m-10) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.1165 time to fit residues: 85.0154 Evaluate side-chains 342 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 167 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.053994 restraints weight = 76906.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056106 restraints weight = 42081.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057600 restraints weight = 27689.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058653 restraints weight = 20407.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059354 restraints weight = 16267.200| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20520 Z= 0.144 Angle : 0.732 13.147 28050 Z= 0.354 Chirality : 0.048 0.367 3387 Planarity : 0.004 0.073 3375 Dihedral : 6.030 54.221 4689 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.49 % Favored : 93.20 % Rotamer: Outliers : 0.05 % Allowed : 0.58 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.31 (0.18), residues: 2310 helix: 0.68 (0.26), residues: 405 sheet: 0.26 (0.18), residues: 714 loop : -0.77 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 66 TYR 0.017 0.001 TYR H 100A PHE 0.030 0.002 PHE J 71 TRP 0.035 0.002 TRP A 427 HIS 0.006 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00328 (20376) covalent geometry : angle 0.69266 (27657) SS BOND : bond 0.00346 ( 39) SS BOND : angle 1.21707 ( 78) hydrogen bonds : bond 0.04081 ( 747) hydrogen bonds : angle 5.67350 ( 1980) link_ALPHA1-2 : bond 0.00384 ( 3) link_ALPHA1-2 : angle 1.78884 ( 9) link_ALPHA1-3 : bond 0.00920 ( 6) link_ALPHA1-3 : angle 1.25838 ( 18) link_ALPHA1-6 : bond 0.00403 ( 3) link_ALPHA1-6 : angle 1.45259 ( 9) link_BETA1-4 : bond 0.00372 ( 39) link_BETA1-4 : angle 1.67288 ( 117) link_NAG-ASN : bond 0.00447 ( 54) link_NAG-ASN : angle 2.78719 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.767 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: A 98 ASN cc_start: 0.9231 (t0) cc_final: 0.8999 (t0) REVERT: A 103 GLN cc_start: 0.9377 (mm110) cc_final: 0.9026 (tp40) REVERT: A 136 ASN cc_start: 0.8766 (m-40) cc_final: 0.8522 (m-40) REVERT: A 256 SER cc_start: 0.8663 (p) cc_final: 0.8406 (p) REVERT: A 426 MET cc_start: 0.8090 (ttt) cc_final: 0.7584 (tmm) REVERT: A 434 MET cc_start: 0.9383 (tpp) cc_final: 0.9086 (tpp) REVERT: A 435 TYR cc_start: 0.8751 (t80) cc_final: 0.7957 (t80) REVERT: B 520 LEU cc_start: 0.8713 (mm) cc_final: 0.8234 (mt) REVERT: B 543 ASN cc_start: 0.9250 (t0) cc_final: 0.8910 (t0) REVERT: B 626 MET cc_start: 0.9027 (mmp) cc_final: 0.8613 (mmm) REVERT: H 61 ASP cc_start: 0.9022 (p0) cc_final: 0.8249 (t0) REVERT: H 80 LEU cc_start: 0.8902 (tp) cc_final: 0.8504 (tp) REVERT: H 82 MET cc_start: 0.8984 (pmm) cc_final: 0.8683 (pmm) REVERT: L 4 MET cc_start: 0.8558 (mmm) cc_final: 0.8329 (mmm) REVERT: L 37 GLN cc_start: 0.9092 (pp30) cc_final: 0.8723 (pp30) REVERT: C 95 MET cc_start: 0.9213 (pmm) cc_final: 0.8860 (pmm) REVERT: C 136 ASN cc_start: 0.8815 (m-40) cc_final: 0.8585 (m-40) REVERT: C 161 MET cc_start: 0.9036 (tpp) cc_final: 0.8789 (tpp) REVERT: C 256 SER cc_start: 0.8411 (m) cc_final: 0.8144 (m) REVERT: C 435 TYR cc_start: 0.8598 (t80) cc_final: 0.7877 (t80) REVERT: C 477 ASP cc_start: 0.9132 (m-30) cc_final: 0.8805 (p0) REVERT: E 584 GLU cc_start: 0.9283 (tt0) cc_final: 0.9045 (tt0) REVERT: E 589 ASP cc_start: 0.9205 (m-30) cc_final: 0.8921 (m-30) REVERT: E 591 GLN cc_start: 0.9497 (tp40) cc_final: 0.8982 (tp40) REVERT: E 598 CYS cc_start: 0.7180 (m) cc_final: 0.6906 (m) REVERT: E 626 MET cc_start: 0.9008 (mmp) cc_final: 0.8643 (mmm) REVERT: E 634 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8898 (tt0) REVERT: G 61 ASP cc_start: 0.9106 (p0) cc_final: 0.8438 (t0) REVERT: J 29 ILE cc_start: 0.9592 (pt) cc_final: 0.9375 (tt) REVERT: J 32 ASN cc_start: 0.8947 (m-40) cc_final: 0.8747 (m-40) REVERT: J 37 GLN cc_start: 0.9138 (pp30) cc_final: 0.8773 (pp30) REVERT: D 95 MET cc_start: 0.9205 (pmm) cc_final: 0.8896 (pmm) REVERT: D 104 MET cc_start: 0.9756 (ttt) cc_final: 0.9519 (ttt) REVERT: D 107 ASP cc_start: 0.9222 (m-30) cc_final: 0.8964 (m-30) REVERT: D 111 LEU cc_start: 0.9514 (tt) cc_final: 0.9297 (pp) REVERT: D 173 TYR cc_start: 0.8203 (p90) cc_final: 0.7937 (p90) REVERT: D 201 ILE cc_start: 0.9040 (mp) cc_final: 0.8755 (tp) REVERT: D 260 LEU cc_start: 0.9250 (mt) cc_final: 0.8509 (mp) REVERT: D 435 TYR cc_start: 0.8519 (t80) cc_final: 0.7689 (t80) REVERT: D 475 MET cc_start: 0.8321 (mmt) cc_final: 0.7950 (mmt) REVERT: F 520 LEU cc_start: 0.8603 (mm) cc_final: 0.8041 (mt) REVERT: F 530 MET cc_start: 0.9141 (tpp) cc_final: 0.8854 (tpp) REVERT: F 543 ASN cc_start: 0.9241 (t0) cc_final: 0.8806 (t0) REVERT: F 621 GLU cc_start: 0.8247 (tp30) cc_final: 0.7679 (tp30) REVERT: F 626 MET cc_start: 0.9193 (mmp) cc_final: 0.8649 (mmm) REVERT: I 61 ASP cc_start: 0.9008 (p0) cc_final: 0.8404 (t0) REVERT: I 80 LEU cc_start: 0.8947 (tp) cc_final: 0.8126 (tp) REVERT: I 82 MET cc_start: 0.8759 (pmm) cc_final: 0.8382 (pmm) REVERT: K 37 GLN cc_start: 0.8933 (pp30) cc_final: 0.8698 (pp30) REVERT: K 71 PHE cc_start: 0.8947 (m-80) cc_final: 0.8651 (m-10) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.1188 time to fit residues: 88.5213 Evaluate side-chains 353 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.053684 restraints weight = 78300.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055826 restraints weight = 42349.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057358 restraints weight = 27717.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058440 restraints weight = 20328.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059219 restraints weight = 16148.314| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20520 Z= 0.152 Angle : 0.739 13.255 28050 Z= 0.360 Chirality : 0.048 0.346 3387 Planarity : 0.004 0.062 3375 Dihedral : 5.944 53.973 4689 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2310 helix: 0.77 (0.27), residues: 405 sheet: 0.17 (0.18), residues: 723 loop : -0.87 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 83 TYR 0.017 0.001 TYR H 100A PHE 0.026 0.002 PHE I 91 TRP 0.038 0.002 TRP L 35 HIS 0.012 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00346 (20376) covalent geometry : angle 0.70066 (27657) SS BOND : bond 0.00364 ( 39) SS BOND : angle 1.20929 ( 78) hydrogen bonds : bond 0.04078 ( 747) hydrogen bonds : angle 5.67691 ( 1980) link_ALPHA1-2 : bond 0.00393 ( 3) link_ALPHA1-2 : angle 1.75756 ( 9) link_ALPHA1-3 : bond 0.00844 ( 6) link_ALPHA1-3 : angle 1.26462 ( 18) link_ALPHA1-6 : bond 0.00374 ( 3) link_ALPHA1-6 : angle 1.48914 ( 9) link_BETA1-4 : bond 0.00343 ( 39) link_BETA1-4 : angle 1.66307 ( 117) link_NAG-ASN : bond 0.00446 ( 54) link_NAG-ASN : angle 2.75480 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.772 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: A 98 ASN cc_start: 0.9179 (t0) cc_final: 0.8921 (t0) REVERT: A 103 GLN cc_start: 0.9293 (mm110) cc_final: 0.8958 (tp40) REVERT: A 256 SER cc_start: 0.8660 (p) cc_final: 0.8378 (p) REVERT: A 435 TYR cc_start: 0.8774 (t80) cc_final: 0.7820 (t80) REVERT: B 520 LEU cc_start: 0.8795 (mm) cc_final: 0.8340 (mt) REVERT: B 530 MET cc_start: 0.8121 (tpp) cc_final: 0.7168 (tpp) REVERT: B 543 ASN cc_start: 0.9341 (t0) cc_final: 0.9003 (t0) REVERT: B 626 MET cc_start: 0.9058 (mmp) cc_final: 0.8660 (mmm) REVERT: H 61 ASP cc_start: 0.9116 (p0) cc_final: 0.8372 (t0) REVERT: H 80 LEU cc_start: 0.8772 (tp) cc_final: 0.8062 (tp) REVERT: H 82 MET cc_start: 0.9034 (pmm) cc_final: 0.8663 (pmm) REVERT: L 18 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8983 (mmmt) REVERT: L 37 GLN cc_start: 0.9106 (pp30) cc_final: 0.8738 (pp30) REVERT: L 53 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8368 (tp-100) REVERT: C 66 HIS cc_start: 0.8261 (m-70) cc_final: 0.7967 (m-70) REVERT: C 95 MET cc_start: 0.9205 (pmm) cc_final: 0.8847 (pmm) REVERT: C 98 ASN cc_start: 0.9331 (t0) cc_final: 0.9115 (t0) REVERT: C 136 ASN cc_start: 0.8867 (m-40) cc_final: 0.8612 (m-40) REVERT: C 256 SER cc_start: 0.8434 (m) cc_final: 0.8181 (m) REVERT: C 434 MET cc_start: 0.8791 (ttm) cc_final: 0.8528 (ttm) REVERT: C 435 TYR cc_start: 0.8628 (t80) cc_final: 0.7948 (t80) REVERT: E 520 LEU cc_start: 0.8686 (mm) cc_final: 0.8167 (mt) REVERT: E 584 GLU cc_start: 0.9320 (tt0) cc_final: 0.9077 (tt0) REVERT: E 589 ASP cc_start: 0.9229 (m-30) cc_final: 0.8938 (m-30) REVERT: E 591 GLN cc_start: 0.9504 (tp40) cc_final: 0.8937 (tp40) REVERT: E 598 CYS cc_start: 0.7309 (m) cc_final: 0.7031 (m) REVERT: E 626 MET cc_start: 0.9027 (mmp) cc_final: 0.8668 (mmm) REVERT: E 634 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8948 (tt0) REVERT: G 61 ASP cc_start: 0.9109 (p0) cc_final: 0.8402 (t0) REVERT: G 78 LEU cc_start: 0.8825 (mt) cc_final: 0.8567 (mt) REVERT: J 37 GLN cc_start: 0.9159 (pp30) cc_final: 0.8741 (pp30) REVERT: J 53 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8378 (tp-100) REVERT: D 95 MET cc_start: 0.9228 (pmm) cc_final: 0.8919 (pmm) REVERT: D 98 ASN cc_start: 0.9299 (t0) cc_final: 0.9093 (t0) REVERT: D 104 MET cc_start: 0.9764 (ttt) cc_final: 0.9479 (ttt) REVERT: D 107 ASP cc_start: 0.9245 (m-30) cc_final: 0.8991 (m-30) REVERT: D 111 LEU cc_start: 0.9518 (tt) cc_final: 0.9303 (pp) REVERT: D 173 TYR cc_start: 0.8160 (p90) cc_final: 0.7929 (p90) REVERT: D 201 ILE cc_start: 0.9046 (mp) cc_final: 0.8760 (tp) REVERT: D 260 LEU cc_start: 0.9181 (mt) cc_final: 0.8460 (mp) REVERT: D 435 TYR cc_start: 0.8563 (t80) cc_final: 0.8009 (t80) REVERT: D 475 MET cc_start: 0.8368 (mmt) cc_final: 0.8013 (mmt) REVERT: F 530 MET cc_start: 0.9156 (tpp) cc_final: 0.8902 (tpp) REVERT: F 543 ASN cc_start: 0.9399 (t0) cc_final: 0.8933 (t0) REVERT: F 548 ILE cc_start: 0.9000 (tp) cc_final: 0.8444 (tp) REVERT: F 621 GLU cc_start: 0.8350 (tp30) cc_final: 0.7743 (tp30) REVERT: F 626 MET cc_start: 0.9109 (mmp) cc_final: 0.8649 (mmm) REVERT: I 61 ASP cc_start: 0.9048 (p0) cc_final: 0.8385 (t0) REVERT: I 80 LEU cc_start: 0.8864 (tp) cc_final: 0.8065 (tp) REVERT: I 82 MET cc_start: 0.8754 (pmm) cc_final: 0.8331 (pmm) REVERT: K 37 GLN cc_start: 0.8940 (pp30) cc_final: 0.8713 (pp30) REVERT: K 71 PHE cc_start: 0.8962 (m-80) cc_final: 0.8722 (m-10) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1160 time to fit residues: 83.8411 Evaluate side-chains 355 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 107 optimal weight: 0.0470 chunk 155 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.053107 restraints weight = 80252.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055177 restraints weight = 44744.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056650 restraints weight = 29829.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057685 restraints weight = 22160.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058318 restraints weight = 17845.101| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20520 Z= 0.175 Angle : 0.756 13.366 28050 Z= 0.369 Chirality : 0.048 0.333 3387 Planarity : 0.004 0.058 3375 Dihedral : 6.050 53.857 4689 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.23 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.49 (0.17), residues: 2310 helix: 0.80 (0.26), residues: 405 sheet: 0.11 (0.18), residues: 723 loop : -0.98 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 66 TYR 0.018 0.002 TYR H 100A PHE 0.028 0.002 PHE I 91 TRP 0.086 0.002 TRP A 427 HIS 0.010 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00399 (20376) covalent geometry : angle 0.71667 (27657) SS BOND : bond 0.00500 ( 39) SS BOND : angle 1.53027 ( 78) hydrogen bonds : bond 0.04162 ( 747) hydrogen bonds : angle 5.69743 ( 1980) link_ALPHA1-2 : bond 0.00382 ( 3) link_ALPHA1-2 : angle 1.73523 ( 9) link_ALPHA1-3 : bond 0.00864 ( 6) link_ALPHA1-3 : angle 1.28226 ( 18) link_ALPHA1-6 : bond 0.00331 ( 3) link_ALPHA1-6 : angle 1.54003 ( 9) link_BETA1-4 : bond 0.00316 ( 39) link_BETA1-4 : angle 1.69151 ( 117) link_NAG-ASN : bond 0.00428 ( 54) link_NAG-ASN : angle 2.76018 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.26 seconds wall clock time: 54 minutes 52.13 seconds (3292.13 seconds total)