Starting phenix.real_space_refine on Sun May 3 20:49:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvv_49865/05_2026/9nvv_49865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvv_49865/05_2026/9nvv_49865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nvv_49865/05_2026/9nvv_49865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvv_49865/05_2026/9nvv_49865.map" model { file = "/net/cci-nas-00/data/ceres_data/9nvv_49865/05_2026/9nvv_49865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvv_49865/05_2026/9nvv_49865.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 102 5.16 5 C 9533 2.51 5 N 2530 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15284 Number of models: 1 Model: "" Number of chains: 49 Chain: "b" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "c" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "d" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "e" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "g" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "b" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "f" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 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: 3.75, per 1000 atoms: 0.25 Number of scatterers: 15284 At special positions: 0 Unit cell: (130.31, 131.97, 121.18, 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 102 16.00 O 3119 8.00 N 2530 7.00 C 9533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.04 Simple disulfide: pdb=" SG CYS b 119 " - pdb=" SG CYS b 205 " distance=2.03 Simple disulfide: pdb=" SG CYS b 126 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS b 131 " - pdb=" SG CYS b 157 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 433 " distance=2.03 Simple disulfide: pdb=" SG CYS b 218 " - pdb=" SG CYS b 247 " distance=2.03 Simple disulfide: pdb=" SG CYS b 228 " - pdb=" SG CYS b 239 " distance=2.03 Simple disulfide: pdb=" SG CYS b 296 " - pdb=" SG CYS b 331 " distance=2.03 Simple disulfide: pdb=" SG CYS b 378 " - pdb=" SG CYS b 445 " distance=2.03 Simple disulfide: pdb=" SG CYS b 385 " - pdb=" SG CYS b 418 " distance=2.03 Simple disulfide: pdb=" SG CYS b 501 " - pdb=" SG CYS c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.04 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " 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=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 501 " - pdb=" SG CYS e 605 " distance=2.03 Simple disulfide: pdb=" SG CYS e 598 " - pdb=" SG CYS e 604 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.02 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.03 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " BETA1-4 " 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 C 2 " - " BMA C 3 " " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG 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-ASN " NAG A 1 " - " ASN b 392 " " NAG B 1 " - " ASN b 332 " " NAG C 1 " - " ASN b 262 " " NAG D 1 " - " ASN b 156 " " NAG E 1 " - " ASN b 160 " " NAG F 1 " - " ASN b 197 " " NAG G 1 " - " ASN b 234 " " NAG H 1 " - " ASN b 241 " " NAG I 1 " - " ASN b 276 " " NAG J 1 " - " ASN b 301 " " NAG K 1 " - " ASN b 448 " " NAG L 1 " - " ASN b 465 " " NAG M 1 " - " ASN d 392 " " NAG N 1 " - " ASN d 332 " " NAG O 1 " - " ASN d 262 " " NAG P 1 " - " ASN d 156 " " NAG Q 1 " - " ASN d 160 " " NAG R 1 " - " ASN d 197 " " NAG S 1 " - " ASN d 234 " " NAG T 1 " - " ASN d 241 " " NAG U 1 " - " ASN d 276 " " NAG V 1 " - " ASN d 301 " " NAG W 1 " - " ASN d 386 " " NAG X 1 " - " ASN d 448 " " NAG Y 1 " - " ASN d 465 " " NAG Z 1 " - " ASN f 392 " " NAG a 1 " - " ASN f 332 " " NAG b 901 " - " ASN b 88 " " NAG b 902 " - " ASN b 133 " " NAG b 903 " - " ASN b 339 " " NAG b 904 " - " ASN b 355 " " NAG b 905 " - " ASN b 269 " " NAG b 906 " - " ASN b 398 " " NAG b 907 " - " ASN b 363 " " NAG b 908 " - " ASN b 386 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 901 " - " ASN d 88 " " NAG d 902 " - " ASN d 133 " " NAG d 903 " - " ASN d 339 " " NAG d 904 " - " ASN d 355 " " NAG d 905 " - " ASN d 269 " " NAG d 906 " - " ASN d 398 " " NAG d 907 " - " ASN d 363 " " NAG e 701 " - " ASN e 611 " " NAG e 702 " - " ASN e 637 " " NAG e 703 " - " ASN e 625 " " NAG f 901 " - " ASN f 88 " " NAG f 902 " - " ASN f 133 " " NAG f 903 " - " ASN f 339 " " NAG f 904 " - " ASN f 355 " " NAG f 905 " - " ASN f 269 " " NAG f 906 " - " ASN f 398 " " NAG f 907 " - " ASN f 363 " " NAG f 908 " - " ASN f 386 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN f 262 " " NAG i 1 " - " ASN f 156 " " NAG j 1 " - " ASN f 160 " " NAG k 1 " - " ASN f 197 " " NAG l 1 " - " ASN f 234 " " NAG m 1 " - " ASN f 241 " " NAG n 1 " - " ASN f 276 " " NAG o 1 " - " ASN f 301 " " NAG p 1 " - " ASN f 448 " " NAG q 1 " - " ASN f 465 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 574.8 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 29 sheets defined 25.4% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 98 through 117 removed outlier: 4.209A pdb=" N GLU b 102 " --> pdb=" O ASN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 removed outlier: 3.527A pdb=" N LEU b 125 " --> pdb=" O LEU b 122 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS b 126 " --> pdb=" O THR b 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 122 through 126' Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.716A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 475 through 481 removed outlier: 3.911A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 484 No H-bonds generated for 'chain 'b' and resid 482 through 484' Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 4.037A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.697A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 624 Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.994A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE c 635 " --> pdb=" O TRP c 631 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 99 through 117 Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.518A pdb=" N LEU d 125 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 122 through 126' Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.795A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 387 through 390 Processing helix chain 'd' and resid 475 through 484 removed outlier: 3.950A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 4.034A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 569 through 596 removed outlier: 3.728A pdb=" N LYS e 574 " --> pdb=" O VAL e 570 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 625 Processing helix chain 'e' and resid 627 through 636 removed outlier: 3.888A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE e 635 " --> pdb=" O TRP e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 638 through 658 Processing helix chain 'f' and resid 70 through 74 Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.253A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.807A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 475 through 481 removed outlier: 3.950A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) Processing helix chain 'f' and resid 482 through 484 No H-bonds generated for 'chain 'f' and resid 482 through 484' Processing helix chain 'g' and resid 523 through 527 removed outlier: 4.551A pdb=" N GLY g 527 " --> pdb=" O GLY g 524 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 4.038A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN g 543 " --> pdb=" O VAL g 539 " (cutoff:3.500A) Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.746A pdb=" N LYS g 574 " --> pdb=" O VAL g 570 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 624 Processing helix chain 'g' and resid 627 through 636 removed outlier: 3.958A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE g 635 " --> pdb=" O TRP g 631 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.280A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.748A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.265A pdb=" N HIS b 66 " --> pdb=" O SER b 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'b' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'b' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.246A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 259 through 261 removed outlier: 9.973A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE b 382 " --> pdb=" O LYS b 421 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE b 376 " --> pdb=" O PHE b 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 271 through 273 removed outlier: 6.648A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE b 359 " --> pdb=" O PHE b 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 302 through 312 removed outlier: 6.483A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 494 through 499 removed outlier: 5.369A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N CYS e 604 " --> pdb=" O TYR d 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 45 through 47 removed outlier: 4.748A pdb=" N VAL d 242 " --> pdb=" O LEU d 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'd' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.267A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.645A pdb=" N ILE d 443 " --> pdb=" O ARG d 298 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY d 451 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N GLN d 290 " --> pdb=" O GLY d 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N LEU d 453 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N LEU d 288 " --> pdb=" O LEU d 453 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N THR d 455 " --> pdb=" O VAL d 286 " (cutoff:3.500A) removed outlier: 11.360A pdb=" N VAL d 286 " --> pdb=" O THR d 455 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N ASP d 457 " --> pdb=" O ILE d 284 " (cutoff:3.500A) removed outlier: 12.493A pdb=" N ILE d 284 " --> pdb=" O ASP d 457 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE d 376 " --> pdb=" O PHE d 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 271 through 273 removed outlier: 12.493A pdb=" N ILE d 284 " --> pdb=" O ASP d 457 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N ASP d 457 " --> pdb=" O ILE d 284 " (cutoff:3.500A) removed outlier: 11.360A pdb=" N VAL d 286 " --> pdb=" O THR d 455 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N THR d 455 " --> pdb=" O VAL d 286 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N LEU d 288 " --> pdb=" O LEU d 453 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N LEU d 453 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N GLN d 290 " --> pdb=" O GLY d 451 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY d 451 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE d 443 " --> pdb=" O ARG d 298 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR d 467 " --> pdb=" O ASP d 457 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR d 357 " --> pdb=" O GLU d 466 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE d 468 " --> pdb=" O THR d 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE d 359 " --> pdb=" O PHE d 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 302 through 312 removed outlier: 6.410A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 45 through 47 removed outlier: 4.735A pdb=" N VAL f 242 " --> pdb=" O LEU f 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'f' and resid 66 through 67 removed outlier: 6.968A pdb=" N HIS f 66 " --> pdb=" O SER f 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'f' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.242A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 259 through 261 removed outlier: 10.027A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.378A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE f 376 " --> pdb=" O PHE f 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.610A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.378A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 302 through 312 removed outlier: 6.459A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1419 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: 2.73 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4600 1.34 - 1.46: 3904 1.46 - 1.58: 6930 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 15566 Sorted by residual: bond pdb=" N ASN e 651 " pdb=" CA ASN e 651 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.28e+00 bond pdb=" N ASN g 651 " pdb=" CA ASN g 651 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.14e+00 bond pdb=" CA THR d 123 " pdb=" C THR d 123 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.57e+00 bond pdb=" CA ASN f 339 " pdb=" CB ASN f 339 " ideal model delta sigma weight residual 1.530 1.552 -0.021 1.75e-02 3.27e+03 1.50e+00 bond pdb=" CA THR b 123 " pdb=" C THR b 123 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.46e+00 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 20683 2.56 - 5.12: 376 5.12 - 7.67: 32 7.67 - 10.23: 13 10.23 - 12.79: 2 Bond angle restraints: 21106 Sorted by residual: angle pdb=" C ARG g 520 " pdb=" CA ARG g 520 " pdb=" CB ARG g 520 " ideal model delta sigma weight residual 116.54 110.07 6.47 1.15e+00 7.56e-01 3.17e+01 angle pdb=" C TRP b 338 " pdb=" N ASN b 339 " pdb=" CA ASN b 339 " ideal model delta sigma weight residual 121.58 112.58 9.00 1.95e+00 2.63e-01 2.13e+01 angle pdb=" C GLY d 472 " pdb=" N GLY d 473 " pdb=" CA GLY d 473 " ideal model delta sigma weight residual 120.07 127.46 -7.39 1.61e+00 3.86e-01 2.11e+01 angle pdb=" CA ASN f 339 " pdb=" CB ASN f 339 " pdb=" CG ASN f 339 " ideal model delta sigma weight residual 112.60 116.83 -4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" CA ASN d 339 " pdb=" CB ASN d 339 " pdb=" CG ASN d 339 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.00e+00 1.00e+00 1.72e+01 ... (remaining 21101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10010 17.71 - 35.42: 646 35.42 - 53.14: 183 53.14 - 70.85: 59 70.85 - 88.56: 22 Dihedral angle restraints: 10920 sinusoidal: 5961 harmonic: 4959 Sorted by residual: dihedral pdb=" CB CYS b 126 " pdb=" SG CYS b 126 " pdb=" SG CYS b 196 " pdb=" CB CYS b 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS f 126 " pdb=" SG CYS f 126 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.88 -57.88 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS d 126 " pdb=" SG CYS d 126 " pdb=" SG CYS d 196 " pdb=" CB CYS d 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.63 -57.63 1 1.00e+01 1.00e-02 4.46e+01 ... (remaining 10917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2250 0.066 - 0.132: 401 0.132 - 0.198: 37 0.198 - 0.264: 5 0.264 - 0.330: 6 Chirality restraints: 2699 Sorted by residual: chirality pdb=" C1 NAG b 901 " pdb=" ND2 ASN b 88 " pdb=" C2 NAG b 901 " pdb=" O5 NAG b 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG f 901 " pdb=" ND2 ASN f 88 " pdb=" C2 NAG f 901 " pdb=" O5 NAG f 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ASN f 339 " pdb=" N ASN f 339 " pdb=" C ASN f 339 " pdb=" CB ASN f 339 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2696 not shown) Planarity restraints: 2593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA d 497 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO d 498 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO d 498 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO d 498 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY d 312 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO d 313 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO d 313 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO d 313 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY b 312 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO b 313 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO b 313 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO b 313 " -0.024 5.00e-02 4.00e+02 ... (remaining 2590 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 994 2.74 - 3.28: 14825 3.28 - 3.82: 24830 3.82 - 4.36: 29137 4.36 - 4.90: 51140 Nonbonded interactions: 120926 Sorted by model distance: nonbonded pdb=" OG1 THR d 37 " pdb=" O CYS e 604 " model vdw 2.197 3.040 nonbonded pdb=" O LEU b 369 " pdb=" OG1 THR b 373 " model vdw 2.266 3.040 nonbonded pdb=" O LEU f 369 " pdb=" OG1 THR f 373 " model vdw 2.287 3.040 nonbonded pdb=" ND2 ASN c 651 " pdb=" O ILE g 535 " model vdw 2.291 3.120 nonbonded pdb=" O LEU d 369 " pdb=" OG1 THR d 373 " model vdw 2.312 3.040 ... (remaining 120921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'N' selection = chain 'T' selection = chain 'a' selection = chain 'h' selection = chain 'm' } ncs_group { reference = (chain 'b' and resid 33 through 907) selection = chain 'd' selection = (chain 'f' and resid 33 through 907) } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.130 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.003 0.050 15720 Z= 0.163 Angle : 0.945 19.069 21532 Z= 0.459 Chirality : 0.052 0.330 2699 Planarity : 0.004 0.054 2524 Dihedral : 12.718 88.561 7602 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.19), residues: 1680 helix: -0.46 (0.26), residues: 399 sheet: -0.78 (0.27), residues: 345 loop : -1.03 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 644 TYR 0.010 0.001 TYR d 384 PHE 0.024 0.002 PHE c 522 TRP 0.021 0.002 TRP f 479 HIS 0.005 0.001 HIS c 564 Details of bonding type rmsd covalent geometry : bond 0.00331 (15566) covalent geometry : angle 0.84931 (21106) SS BOND : bond 0.00303 ( 36) SS BOND : angle 1.05016 ( 72) hydrogen bonds : bond 0.20393 ( 493) hydrogen bonds : angle 8.39654 ( 1419) link_ALPHA1-3 : bond 0.01159 ( 2) link_ALPHA1-3 : angle 1.52179 ( 6) link_ALPHA1-6 : bond 0.00938 ( 1) link_ALPHA1-6 : angle 1.53346 ( 3) link_BETA1-4 : bond 0.00903 ( 46) link_BETA1-4 : angle 3.60070 ( 138) link_NAG-ASN : bond 0.00408 ( 69) link_NAG-ASN : angle 3.18441 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.595 Fit side-chains REVERT: c 536 THR cc_start: 0.8670 (p) cc_final: 0.8242 (t) REVERT: d 35 TRP cc_start: 0.8790 (m100) cc_final: 0.8093 (m-90) REVERT: e 536 THR cc_start: 0.8644 (p) cc_final: 0.8218 (t) REVERT: f 80 ASN cc_start: 0.9079 (p0) cc_final: 0.8870 (p0) REVERT: g 536 THR cc_start: 0.8501 (p) cc_final: 0.8057 (t) outliers start: 0 outliers final: 1 residues processed: 151 average time/residue: 0.8162 time to fit residues: 132.5730 Evaluate side-chains 85 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 185 ASN e 607 ASN e 651 ASN ** f 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 330 HIS g 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.075847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056646 restraints weight = 39271.330| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.74 r_work: 0.2772 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15720 Z= 0.237 Angle : 0.814 18.534 21532 Z= 0.362 Chirality : 0.048 0.272 2699 Planarity : 0.004 0.042 2524 Dihedral : 8.269 59.603 4295 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.90 % Allowed : 10.04 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.20), residues: 1680 helix: 0.10 (0.27), residues: 408 sheet: -0.90 (0.25), residues: 408 loop : -0.59 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG g 585 TYR 0.012 0.002 TYR e 638 PHE 0.015 0.002 PHE f 383 TRP 0.011 0.002 TRP b 338 HIS 0.002 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00561 (15566) covalent geometry : angle 0.69553 (21106) SS BOND : bond 0.00384 ( 36) SS BOND : angle 1.00763 ( 72) hydrogen bonds : bond 0.05502 ( 493) hydrogen bonds : angle 6.10008 ( 1419) link_ALPHA1-3 : bond 0.00814 ( 2) link_ALPHA1-3 : angle 1.40451 ( 6) link_ALPHA1-6 : bond 0.00625 ( 1) link_ALPHA1-6 : angle 1.91947 ( 3) link_BETA1-4 : bond 0.00646 ( 46) link_BETA1-4 : angle 3.17924 ( 138) link_NAG-ASN : bond 0.00442 ( 69) link_NAG-ASN : angle 3.51525 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.612 Fit side-chains REVERT: c 536 THR cc_start: 0.8855 (p) cc_final: 0.8381 (t) REVERT: c 621 GLU cc_start: 0.8761 (pt0) cc_final: 0.8292 (pp20) REVERT: d 35 TRP cc_start: 0.8735 (m100) cc_final: 0.7751 (m-90) REVERT: d 185 ASN cc_start: 0.8354 (t0) cc_final: 0.8076 (t0) REVERT: e 536 THR cc_start: 0.8826 (p) cc_final: 0.8351 (t) REVERT: e 584 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8289 (mt-10) REVERT: f 80 ASN cc_start: 0.9386 (p0) cc_final: 0.9181 (p0) REVERT: g 536 THR cc_start: 0.8853 (p) cc_final: 0.8384 (t) REVERT: g 621 GLU cc_start: 0.8541 (pt0) cc_final: 0.8053 (pp20) REVERT: g 638 TYR cc_start: 0.8422 (m-80) cc_final: 0.8008 (m-80) outliers start: 29 outliers final: 16 residues processed: 110 average time/residue: 0.6852 time to fit residues: 82.1240 Evaluate side-chains 90 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 599 SER Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 651 ASN d 377 ASN f 280 ASN ** f 377 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 = 0.3357 r_free = 0.3357 target = 0.075008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055697 restraints weight = 39460.141| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.73 r_work: 0.2757 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15720 Z= 0.211 Angle : 0.754 18.157 21532 Z= 0.334 Chirality : 0.047 0.256 2699 Planarity : 0.003 0.028 2524 Dihedral : 8.121 59.965 4293 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.23 % Allowed : 11.09 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.20), residues: 1680 helix: 0.25 (0.28), residues: 399 sheet: -0.67 (0.26), residues: 369 loop : -0.39 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 644 TYR 0.018 0.001 TYR e 638 PHE 0.013 0.002 PHE b 391 TRP 0.011 0.001 TRP b 338 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00500 (15566) covalent geometry : angle 0.64010 (21106) SS BOND : bond 0.00325 ( 36) SS BOND : angle 0.82208 ( 72) hydrogen bonds : bond 0.04814 ( 493) hydrogen bonds : angle 5.56672 ( 1419) link_ALPHA1-3 : bond 0.00741 ( 2) link_ALPHA1-3 : angle 1.18583 ( 6) link_ALPHA1-6 : bond 0.00443 ( 1) link_ALPHA1-6 : angle 1.85444 ( 3) link_BETA1-4 : bond 0.00641 ( 46) link_BETA1-4 : angle 3.08963 ( 138) link_NAG-ASN : bond 0.00440 ( 69) link_NAG-ASN : angle 3.25794 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.579 Fit side-chains REVERT: c 536 THR cc_start: 0.8849 (p) cc_final: 0.8333 (t) REVERT: c 621 GLU cc_start: 0.8728 (pt0) cc_final: 0.8274 (pp20) REVERT: d 35 TRP cc_start: 0.8787 (m100) cc_final: 0.7860 (m-90) REVERT: d 185 ASN cc_start: 0.8375 (t0) cc_final: 0.8043 (t0) REVERT: e 536 THR cc_start: 0.8857 (p) cc_final: 0.8378 (t) REVERT: f 80 ASN cc_start: 0.9391 (p0) cc_final: 0.9183 (p0) REVERT: g 536 THR cc_start: 0.8903 (p) cc_final: 0.8423 (t) REVERT: g 638 TYR cc_start: 0.8467 (m-80) cc_final: 0.8058 (m-80) outliers start: 34 outliers final: 21 residues processed: 114 average time/residue: 0.6690 time to fit residues: 83.4015 Evaluate side-chains 98 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 599 SER Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 0.0770 chunk 93 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 377 ASN f 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057522 restraints weight = 39155.222| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.70 r_work: 0.2806 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15720 Z= 0.112 Angle : 0.679 17.596 21532 Z= 0.298 Chirality : 0.045 0.232 2699 Planarity : 0.003 0.026 2524 Dihedral : 7.948 59.642 4293 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.57 % Allowed : 12.34 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.20), residues: 1680 helix: 0.63 (0.29), residues: 381 sheet: -0.57 (0.26), residues: 363 loop : -0.39 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 519 TYR 0.018 0.001 TYR e 638 PHE 0.015 0.001 PHE c 522 TRP 0.013 0.001 TRP b 338 HIS 0.002 0.000 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00244 (15566) covalent geometry : angle 0.56801 (21106) SS BOND : bond 0.00236 ( 36) SS BOND : angle 0.57145 ( 72) hydrogen bonds : bond 0.04017 ( 493) hydrogen bonds : angle 5.21820 ( 1419) link_ALPHA1-3 : bond 0.00832 ( 2) link_ALPHA1-3 : angle 1.21247 ( 6) link_ALPHA1-6 : bond 0.00501 ( 1) link_ALPHA1-6 : angle 1.66580 ( 3) link_BETA1-4 : bond 0.00661 ( 46) link_BETA1-4 : angle 2.95675 ( 138) link_NAG-ASN : bond 0.00365 ( 69) link_NAG-ASN : angle 3.01303 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.602 Fit side-chains REVERT: c 536 THR cc_start: 0.8848 (p) cc_final: 0.8323 (t) REVERT: c 647 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7525 (mm-30) REVERT: d 35 TRP cc_start: 0.8801 (m100) cc_final: 0.7878 (m-90) REVERT: d 185 ASN cc_start: 0.8349 (t0) cc_final: 0.8019 (t0) REVERT: e 536 THR cc_start: 0.8804 (p) cc_final: 0.8332 (t) REVERT: g 536 THR cc_start: 0.8876 (p) cc_final: 0.8367 (t) REVERT: g 638 TYR cc_start: 0.8458 (m-80) cc_final: 0.8167 (m-80) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.6968 time to fit residues: 80.1372 Evaluate side-chains 91 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055005 restraints weight = 39549.812| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.72 r_work: 0.2748 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15720 Z= 0.246 Angle : 0.748 17.761 21532 Z= 0.334 Chirality : 0.047 0.255 2699 Planarity : 0.003 0.034 2524 Dihedral : 8.089 59.436 4293 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.30 % Allowed : 12.86 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.21), residues: 1680 helix: 0.34 (0.28), residues: 399 sheet: -0.87 (0.24), residues: 396 loop : -0.19 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 644 TYR 0.017 0.001 TYR e 638 PHE 0.015 0.002 PHE c 522 TRP 0.010 0.001 TRP b 96 HIS 0.005 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00586 (15566) covalent geometry : angle 0.64328 (21106) SS BOND : bond 0.00379 ( 36) SS BOND : angle 0.80063 ( 72) hydrogen bonds : bond 0.04454 ( 493) hydrogen bonds : angle 5.30940 ( 1419) link_ALPHA1-3 : bond 0.00639 ( 2) link_ALPHA1-3 : angle 1.27405 ( 6) link_ALPHA1-6 : bond 0.00396 ( 1) link_ALPHA1-6 : angle 1.92579 ( 3) link_BETA1-4 : bond 0.00625 ( 46) link_BETA1-4 : angle 2.96953 ( 138) link_NAG-ASN : bond 0.00435 ( 69) link_NAG-ASN : angle 3.13840 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.590 Fit side-chains REVERT: b 42 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8379 (m) REVERT: c 536 THR cc_start: 0.8891 (p) cc_final: 0.8371 (t) REVERT: c 657 GLU cc_start: 0.7670 (tp30) cc_final: 0.7245 (tt0) REVERT: d 35 TRP cc_start: 0.8826 (m100) cc_final: 0.7918 (m-90) REVERT: d 185 ASN cc_start: 0.8377 (t0) cc_final: 0.8015 (t0) REVERT: e 536 THR cc_start: 0.8882 (p) cc_final: 0.8375 (t) REVERT: e 617 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8706 (mtpm) REVERT: g 536 THR cc_start: 0.8927 (p) cc_final: 0.8432 (t) REVERT: g 621 GLU cc_start: 0.8639 (pt0) cc_final: 0.8313 (pp20) REVERT: g 633 LYS cc_start: 0.8784 (pptt) cc_final: 0.8525 (pptt) REVERT: g 638 TYR cc_start: 0.8513 (m-80) cc_final: 0.8216 (m-80) outliers start: 35 outliers final: 24 residues processed: 110 average time/residue: 0.6768 time to fit residues: 81.6968 Evaluate side-chains 100 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 617 LYS Chi-restraints excluded: chain e residue 620 ASP Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 208 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.0010 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056809 restraints weight = 38939.016| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.70 r_work: 0.2794 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15720 Z= 0.113 Angle : 0.676 17.450 21532 Z= 0.298 Chirality : 0.044 0.230 2699 Planarity : 0.003 0.027 2524 Dihedral : 7.945 59.981 4293 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.03 % Allowed : 13.12 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.21), residues: 1680 helix: 0.69 (0.29), residues: 381 sheet: -0.58 (0.26), residues: 363 loop : -0.32 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.018 0.001 TYR e 638 PHE 0.010 0.001 PHE c 522 TRP 0.015 0.001 TRP b 338 HIS 0.002 0.000 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (15566) covalent geometry : angle 0.56818 (21106) SS BOND : bond 0.00244 ( 36) SS BOND : angle 0.58133 ( 72) hydrogen bonds : bond 0.03969 ( 493) hydrogen bonds : angle 5.09336 ( 1419) link_ALPHA1-3 : bond 0.00746 ( 2) link_ALPHA1-3 : angle 1.24378 ( 6) link_ALPHA1-6 : bond 0.00484 ( 1) link_ALPHA1-6 : angle 1.62964 ( 3) link_BETA1-4 : bond 0.00649 ( 46) link_BETA1-4 : angle 2.89408 ( 138) link_NAG-ASN : bond 0.00359 ( 69) link_NAG-ASN : angle 2.98065 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.653 Fit side-chains REVERT: c 536 THR cc_start: 0.8857 (p) cc_final: 0.8316 (t) REVERT: c 621 GLU cc_start: 0.8684 (pt0) cc_final: 0.8160 (pp20) REVERT: c 647 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7511 (mm-30) REVERT: d 35 TRP cc_start: 0.8824 (m100) cc_final: 0.7914 (m-90) REVERT: d 185 ASN cc_start: 0.8360 (t0) cc_final: 0.8003 (t0) REVERT: e 519 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7648 (pmt-80) REVERT: e 536 THR cc_start: 0.8809 (p) cc_final: 0.8310 (t) REVERT: g 536 THR cc_start: 0.8899 (p) cc_final: 0.8384 (t) REVERT: g 638 TYR cc_start: 0.8501 (m-80) cc_final: 0.8225 (m-80) outliers start: 31 outliers final: 18 residues processed: 110 average time/residue: 0.6577 time to fit residues: 79.5284 Evaluate side-chains 96 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 519 ARG Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055754 restraints weight = 38958.531| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.70 r_work: 0.2761 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15720 Z= 0.183 Angle : 0.713 17.482 21532 Z= 0.315 Chirality : 0.045 0.243 2699 Planarity : 0.003 0.032 2524 Dihedral : 7.965 59.907 4293 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 13.39 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.21), residues: 1680 helix: 0.67 (0.29), residues: 381 sheet: -0.80 (0.25), residues: 390 loop : -0.23 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.017 0.001 TYR e 638 PHE 0.011 0.001 PHE b 317 TRP 0.011 0.001 TRP b 338 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00435 (15566) covalent geometry : angle 0.60897 (21106) SS BOND : bond 0.00300 ( 36) SS BOND : angle 0.99499 ( 72) hydrogen bonds : bond 0.04129 ( 493) hydrogen bonds : angle 5.13127 ( 1419) link_ALPHA1-3 : bond 0.00638 ( 2) link_ALPHA1-3 : angle 1.26840 ( 6) link_ALPHA1-6 : bond 0.00441 ( 1) link_ALPHA1-6 : angle 1.76014 ( 3) link_BETA1-4 : bond 0.00625 ( 46) link_BETA1-4 : angle 2.87999 ( 138) link_NAG-ASN : bond 0.00380 ( 69) link_NAG-ASN : angle 3.00824 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.606 Fit side-chains REVERT: c 536 THR cc_start: 0.8879 (p) cc_final: 0.8345 (t) REVERT: c 621 GLU cc_start: 0.8682 (pt0) cc_final: 0.8155 (pp20) REVERT: c 647 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7528 (mm-30) REVERT: c 657 GLU cc_start: 0.7565 (tp30) cc_final: 0.7094 (tt0) REVERT: d 35 TRP cc_start: 0.8835 (m100) cc_final: 0.7910 (m-90) REVERT: d 185 ASN cc_start: 0.8377 (t0) cc_final: 0.8016 (t0) REVERT: e 519 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7647 (pmt-80) REVERT: e 536 THR cc_start: 0.8843 (p) cc_final: 0.8343 (t) REVERT: g 536 THR cc_start: 0.8919 (p) cc_final: 0.8401 (t) REVERT: g 633 LYS cc_start: 0.8770 (pptt) cc_final: 0.8519 (pptt) REVERT: g 638 TYR cc_start: 0.8488 (m-80) cc_final: 0.8252 (m-80) outliers start: 34 outliers final: 23 residues processed: 111 average time/residue: 0.6143 time to fit residues: 75.2972 Evaluate side-chains 98 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 599 SER Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 463 ASN Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 519 ARG Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 620 ASP Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 208 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.055857 restraints weight = 39198.057| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.70 r_work: 0.2761 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15720 Z= 0.170 Angle : 0.709 17.436 21532 Z= 0.313 Chirality : 0.045 0.242 2699 Planarity : 0.003 0.034 2524 Dihedral : 7.967 59.732 4293 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 13.91 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1680 helix: 0.68 (0.29), residues: 381 sheet: -0.64 (0.26), residues: 351 loop : -0.28 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.017 0.001 TYR e 638 PHE 0.011 0.001 PHE b 317 TRP 0.012 0.001 TRP b 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00404 (15566) covalent geometry : angle 0.60476 (21106) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.10647 ( 72) hydrogen bonds : bond 0.04112 ( 493) hydrogen bonds : angle 5.11735 ( 1419) link_ALPHA1-3 : bond 0.00635 ( 2) link_ALPHA1-3 : angle 1.27134 ( 6) link_ALPHA1-6 : bond 0.00402 ( 1) link_ALPHA1-6 : angle 1.66665 ( 3) link_BETA1-4 : bond 0.00618 ( 46) link_BETA1-4 : angle 2.85896 ( 138) link_NAG-ASN : bond 0.00375 ( 69) link_NAG-ASN : angle 2.99404 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.565 Fit side-chains REVERT: b 42 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8338 (m) REVERT: c 536 THR cc_start: 0.8873 (p) cc_final: 0.8337 (t) REVERT: c 621 GLU cc_start: 0.8692 (pt0) cc_final: 0.8190 (pp20) REVERT: c 647 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7581 (mm-30) REVERT: d 35 TRP cc_start: 0.8838 (m100) cc_final: 0.7919 (m-90) REVERT: d 185 ASN cc_start: 0.8383 (t0) cc_final: 0.8025 (t0) REVERT: e 519 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7608 (pmt-80) REVERT: e 536 THR cc_start: 0.8836 (p) cc_final: 0.8332 (t) REVERT: g 536 THR cc_start: 0.8914 (p) cc_final: 0.8395 (t) REVERT: g 633 LYS cc_start: 0.8767 (pptt) cc_final: 0.8472 (pptt) REVERT: g 638 TYR cc_start: 0.8470 (m-80) cc_final: 0.8255 (m-80) outliers start: 32 outliers final: 26 residues processed: 107 average time/residue: 0.6369 time to fit residues: 74.7176 Evaluate side-chains 100 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 599 SER Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 463 ASN Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 519 ARG Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 620 ASP Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 208 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 2.9990 chunk 148 optimal weight: 0.0570 chunk 122 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.076068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.057170 restraints weight = 38752.342| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.56 r_work: 0.2821 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15720 Z= 0.152 Angle : 0.702 17.389 21532 Z= 0.311 Chirality : 0.045 0.239 2699 Planarity : 0.003 0.052 2524 Dihedral : 7.949 59.923 4293 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.97 % Allowed : 13.98 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.20), residues: 1680 helix: 0.70 (0.29), residues: 381 sheet: -0.55 (0.27), residues: 330 loop : -0.36 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG g 519 TYR 0.017 0.001 TYR e 638 PHE 0.010 0.001 PHE b 317 TRP 0.012 0.001 TRP b 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00357 (15566) covalent geometry : angle 0.59969 (21106) SS BOND : bond 0.00275 ( 36) SS BOND : angle 0.94934 ( 72) hydrogen bonds : bond 0.04038 ( 493) hydrogen bonds : angle 5.09439 ( 1419) link_ALPHA1-3 : bond 0.00637 ( 2) link_ALPHA1-3 : angle 1.27974 ( 6) link_ALPHA1-6 : bond 0.00401 ( 1) link_ALPHA1-6 : angle 1.62536 ( 3) link_BETA1-4 : bond 0.00621 ( 46) link_BETA1-4 : angle 2.83558 ( 138) link_NAG-ASN : bond 0.00369 ( 69) link_NAG-ASN : angle 2.96718 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.540 Fit side-chains REVERT: c 536 THR cc_start: 0.8973 (p) cc_final: 0.8447 (t) REVERT: c 621 GLU cc_start: 0.8638 (pt0) cc_final: 0.8213 (pp20) REVERT: c 647 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7793 (mm-30) REVERT: c 657 GLU cc_start: 0.7633 (tp30) cc_final: 0.7279 (tt0) REVERT: d 35 TRP cc_start: 0.8967 (m100) cc_final: 0.8193 (m-90) REVERT: d 185 ASN cc_start: 0.8309 (t0) cc_final: 0.8027 (t0) REVERT: e 519 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7598 (pmt-80) REVERT: e 536 THR cc_start: 0.8911 (p) cc_final: 0.8422 (t) REVERT: g 536 THR cc_start: 0.9003 (p) cc_final: 0.8507 (t) REVERT: g 620 ASP cc_start: 0.8538 (t0) cc_final: 0.8228 (p0) REVERT: g 633 LYS cc_start: 0.8686 (pptt) cc_final: 0.8384 (pptt) outliers start: 30 outliers final: 26 residues processed: 105 average time/residue: 0.6491 time to fit residues: 74.9960 Evaluate side-chains 102 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 208 VAL Chi-restraints excluded: chain d residue 463 ASN Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 519 ARG Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 620 ASP Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 208 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.074842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.055937 restraints weight = 39233.089| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.52 r_work: 0.2773 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15720 Z= 0.236 Angle : 0.749 17.508 21532 Z= 0.335 Chirality : 0.046 0.257 2699 Planarity : 0.003 0.046 2524 Dihedral : 8.047 58.936 4293 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.97 % Allowed : 14.11 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.21), residues: 1680 helix: 0.60 (0.29), residues: 381 sheet: -0.87 (0.24), residues: 390 loop : -0.21 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG g 519 TYR 0.016 0.001 TYR e 638 PHE 0.013 0.002 PHE b 317 TRP 0.011 0.001 TRP e 631 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00563 (15566) covalent geometry : angle 0.65075 (21106) SS BOND : bond 0.00359 ( 36) SS BOND : angle 1.07848 ( 72) hydrogen bonds : bond 0.04354 ( 493) hydrogen bonds : angle 5.20276 ( 1419) link_ALPHA1-3 : bond 0.00575 ( 2) link_ALPHA1-3 : angle 1.29398 ( 6) link_ALPHA1-6 : bond 0.00346 ( 1) link_ALPHA1-6 : angle 1.72046 ( 3) link_BETA1-4 : bond 0.00601 ( 46) link_BETA1-4 : angle 2.85318 ( 138) link_NAG-ASN : bond 0.00412 ( 69) link_NAG-ASN : angle 3.04993 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.623 Fit side-chains REVERT: b 42 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8500 (m) REVERT: c 536 THR cc_start: 0.8986 (p) cc_final: 0.8471 (t) REVERT: c 621 GLU cc_start: 0.8702 (pt0) cc_final: 0.8230 (pp20) REVERT: c 647 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7696 (mm-30) REVERT: c 648 GLU cc_start: 0.8000 (pp20) cc_final: 0.7698 (pm20) REVERT: c 657 GLU cc_start: 0.7650 (tp30) cc_final: 0.7310 (tt0) REVERT: d 35 TRP cc_start: 0.8940 (m100) cc_final: 0.8116 (m-90) REVERT: d 185 ASN cc_start: 0.8376 (t0) cc_final: 0.8049 (t0) REVERT: e 519 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7608 (pmt-80) REVERT: e 536 THR cc_start: 0.8927 (p) cc_final: 0.8436 (t) REVERT: e 633 LYS cc_start: 0.8712 (pmtt) cc_final: 0.8210 (pmmt) REVERT: g 536 THR cc_start: 0.9003 (p) cc_final: 0.8502 (t) REVERT: g 620 ASP cc_start: 0.8603 (t0) cc_final: 0.8254 (p0) outliers start: 30 outliers final: 27 residues processed: 102 average time/residue: 0.6438 time to fit residues: 72.4229 Evaluate side-chains 99 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 546 SER Chi-restraints excluded: chain c residue 599 SER Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 208 VAL Chi-restraints excluded: chain d residue 463 ASN Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 519 ARG Chi-restraints excluded: chain e residue 539 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 620 ASP Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 208 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 539 VAL Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057534 restraints weight = 38545.378| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.54 r_work: 0.2817 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15720 Z= 0.127 Angle : 0.698 17.358 21532 Z= 0.310 Chirality : 0.045 0.237 2699 Planarity : 0.003 0.048 2524 Dihedral : 7.956 59.682 4293 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.84 % Allowed : 14.37 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1680 helix: 0.66 (0.29), residues: 381 sheet: -0.54 (0.27), residues: 330 loop : -0.34 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG g 519 TYR 0.017 0.001 TYR g 638 PHE 0.009 0.001 PHE c 522 TRP 0.015 0.001 TRP b 338 HIS 0.003 0.000 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00290 (15566) covalent geometry : angle 0.59787 (21106) SS BOND : bond 0.00263 ( 36) SS BOND : angle 0.86739 ( 72) hydrogen bonds : bond 0.03998 ( 493) hydrogen bonds : angle 5.09301 ( 1419) link_ALPHA1-3 : bond 0.00642 ( 2) link_ALPHA1-3 : angle 1.29904 ( 6) link_ALPHA1-6 : bond 0.00406 ( 1) link_ALPHA1-6 : angle 1.54424 ( 3) link_BETA1-4 : bond 0.00620 ( 46) link_BETA1-4 : angle 2.80257 ( 138) link_NAG-ASN : bond 0.00360 ( 69) link_NAG-ASN : angle 2.94443 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.54 seconds wall clock time: 66 minutes 49.79 seconds (4009.79 seconds total)