Starting phenix.real_space_refine on Thu Sep 18 12:34:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btl_44893/09_2025/9btl_44893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btl_44893/09_2025/9btl_44893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btl_44893/09_2025/9btl_44893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btl_44893/09_2025/9btl_44893.map" model { file = "/net/cci-nas-00/data/ceres_data/9btl_44893/09_2025/9btl_44893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btl_44893/09_2025/9btl_44893.cif" } resolution = 2.96 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= 0.015 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 113 5.16 5 C 10404 2.51 5 N 2757 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16688 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3463 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "H" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "I" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3471 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "K" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "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: 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "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: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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 Time building chain proxies: 4.51, per 1000 atoms: 0.27 Number of scatterers: 16688 At special positions: 0 Unit cell: (123.67, 122.84, 156.87, 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 113 16.00 O 3414 8.00 N 2757 7.00 C 10404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.13 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=1.76 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.06 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.22 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A 601 " - " ASN A 448 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 234 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 137 " " NAG B 701 " - " ASN B 637 " " NAG C 1 " - " ASN A 363 " " NAG D 1 " - " ASN A 392 " " NAG E 601 " - " ASN E 276 " " NAG E 602 " - " ASN E 355 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 386 " " NAG I 601 " - " ASN I 448 " " NAG I 602 " - " ASN I 276 " " NAG I 603 " - " ASN I 355 " " NAG I 604 " - " ASN I 88 " " NAG I 605 " - " ASN I 339 " " NAG I 606 " - " ASN I 145 " " NAG J 701 " - " ASN J 618 " " NAG J 702 " - " ASN J 637 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 355 " " NAG N 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN E 363 " " NAG T 1 " - " ASN E 392 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN E 295 " " NAG X 1 " - " ASN E 160 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 197 " " NAG a 1 " - " ASN E 88 " " NAG b 1 " - " ASN E 332 " " NAG c 1 " - " ASN E 301 " " NAG d 1 " - " ASN E 448 " " NAG e 1 " - " ASN E 234 " " NAG f 1 " - " ASN I 363 " " NAG g 1 " - " ASN I 392 " " NAG h 1 " - " ASN I 386 " " NAG i 1 " - " ASN I 262 " " NAG j 1 " - " ASN I 295 " " NAG k 1 " - " ASN I 160 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 197 " " NAG n 1 " - " ASN I 133 " " NAG o 1 " - " ASN I 332 " " NAG p 1 " - " ASN I 301 " " NAG q 1 " - " ASN I 234 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 849.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 37 sheets defined 24.1% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.560A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.741A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.188A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.897A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.708A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 removed outlier: 3.569A pdb=" N GLU B 621 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.522A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.252A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.839A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.573A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.845A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.556A pdb=" N ASN E 462 " --> pdb=" O GLY E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 481 removed outlier: 4.132A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.772A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.868A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.730A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.710A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 664 removed outlier: 3.568A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.016A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100J through 100M Processing helix chain 'I' and resid 99 through 116 Processing helix chain 'I' and resid 335 through 354 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.962A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 removed outlier: 4.543A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 595 Processing helix chain 'J' and resid 618 through 626 removed outlier: 3.687A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP J 624 " --> pdb=" O SER J 620 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET J 626 " --> pdb=" O ILE J 622 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.943A pdb=" N TRP J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.764A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.748A pdb=" N GLU L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 3.572A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.775A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.767A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.820A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.431A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 424 " --> pdb=" O MET A 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.256A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 298 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 removed outlier: 3.504A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.687A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.250A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 298 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.816A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 374 through 375 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.751A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.551A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.403A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 7.308A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.877A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 271 through 274 removed outlier: 11.220A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.877A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.907A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.550A pdb=" N ASN H 58 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP H 35 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR H 33 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AC7, first strand: chain 'I' and resid 494 through 499 Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.650A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.822A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 120 through 121 removed outlier: 4.128A pdb=" N VAL I 120 " --> pdb=" O GLN I 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.658A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.573A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS I 378 " --> pdb=" O GLU I 381 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.635A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 304 through 312 removed outlier: 7.039A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AD8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.598A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.598A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5162 1.35 - 1.47: 4400 1.47 - 1.60: 7292 1.60 - 1.73: 0 1.73 - 1.86: 150 Bond restraints: 17004 Sorted by residual: bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.334 1.367 -0.034 8.40e-03 1.42e+04 1.63e+01 bond pdb=" C THR A 139 " pdb=" O THR A 139 " ideal model delta sigma weight residual 1.234 1.279 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" N TYR F 638 " pdb=" CA TYR F 638 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.35e-02 5.49e+03 8.00e+00 bond pdb=" N LEU A 122 " pdb=" CA LEU A 122 " ideal model delta sigma weight residual 1.462 1.494 -0.033 1.15e-02 7.56e+03 8.00e+00 bond pdb=" N ILE F 641 " pdb=" CA ILE F 641 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.51e+00 ... (remaining 16999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 22771 3.46 - 6.93: 264 6.93 - 10.39: 41 10.39 - 13.85: 6 13.85 - 17.32: 2 Bond angle restraints: 23084 Sorted by residual: angle pdb=" C CYS E 54 " pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " ideal model delta sigma weight residual 113.33 96.01 17.32 2.26e+00 1.96e-01 5.87e+01 angle pdb=" CA GLU B 621 " pdb=" CB GLU B 621 " pdb=" CG GLU B 621 " ideal model delta sigma weight residual 114.10 126.80 -12.70 2.00e+00 2.50e-01 4.03e+01 angle pdb=" CA CYS I 501 " pdb=" CB CYS I 501 " pdb=" SG CYS I 501 " ideal model delta sigma weight residual 114.40 127.28 -12.88 2.30e+00 1.89e-01 3.14e+01 angle pdb=" C GLU B 621 " pdb=" CA GLU B 621 " pdb=" CB GLU B 621 " ideal model delta sigma weight residual 111.02 120.00 -8.98 1.62e+00 3.81e-01 3.07e+01 angle pdb=" C CYS E 119 " pdb=" N VAL E 120 " pdb=" CA VAL E 120 " ideal model delta sigma weight residual 120.69 128.17 -7.48 1.46e+00 4.69e-01 2.62e+01 ... (remaining 23079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10545 17.85 - 35.70: 783 35.70 - 53.55: 214 53.55 - 71.41: 60 71.41 - 89.26: 19 Dihedral angle restraints: 11621 sinusoidal: 6048 harmonic: 5573 Sorted by residual: dihedral pdb=" C CYS E 54 " pdb=" N CYS E 54 " pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " ideal model delta harmonic sigma weight residual -122.60 -105.00 -17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.32 54.32 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 141.34 -48.34 1 1.00e+01 1.00e-02 3.22e+01 ... (remaining 11618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2539 0.086 - 0.172: 335 0.172 - 0.259: 29 0.259 - 0.345: 6 0.345 - 0.431: 3 Chirality restraints: 2912 Sorted by residual: chirality pdb=" CG LEU J 544 " pdb=" CB LEU J 544 " pdb=" CD1 LEU J 544 " pdb=" CD2 LEU J 544 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C3 BMA l 3 " pdb=" C2 BMA l 3 " pdb=" C4 BMA l 3 " pdb=" O3 BMA l 3 " both_signs ideal model delta sigma weight residual False 2.41 2.01 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA CYS E 54 " pdb=" N CYS E 54 " pdb=" C CYS E 54 " pdb=" CB CYS E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 2909 not shown) Planarity restraints: 2850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 605 " -0.209 2.00e-02 2.50e+03 1.74e-01 3.77e+02 pdb=" C7 NAG E 605 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG E 605 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG E 605 " 0.286 2.00e-02 2.50e+03 pdb=" O7 NAG E 605 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 608 " -0.170 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" C7 NAG A 608 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A 608 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A 608 " 0.240 2.00e-02 2.50e+03 pdb=" O7 NAG A 608 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 133 " -0.019 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASN A 133 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 133 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL A 134 " -0.023 2.00e-02 2.50e+03 ... (remaining 2847 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2442 2.77 - 3.30: 14805 3.30 - 3.83: 27359 3.83 - 4.37: 31173 4.37 - 4.90: 55073 Nonbonded interactions: 130852 Sorted by model distance: nonbonded pdb=" O VAL I 36 " pdb=" OG1 THR J 606 " model vdw 2.232 3.040 nonbonded pdb=" O ASP J 632 " pdb=" OG SER J 636 " model vdw 2.274 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.323 3.040 nonbonded pdb=" OG SER J 620 " pdb=" O6 NAG J 701 " model vdw 2.332 3.040 ... (remaining 130847 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' and (resid 33 through 185 or resid 189 through 605)) selection = (chain 'E' and (resid 33 through 185 or resid 189 through 605)) selection = (chain 'I' and (resid 33 through 185 or resid 189 through 397 or resid 412 throu \ gh 605)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 520 through 701) selection = (chain 'J' and (resid 520 through 545 or resid 568 through 701)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'K' selection = chain 'V' selection = chain 'X' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'O' selection = chain 'i' } 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: 0.000 Normalize map: mean=0, sd=1: 4.810 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.930 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.271 17151 Z= 0.283 Angle : 1.072 25.702 23487 Z= 0.568 Chirality : 0.056 0.431 2912 Planarity : 0.007 0.174 2791 Dihedral : 13.310 89.256 7905 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.06 % Allowed : 12.57 % Favored : 87.38 % Cbeta Deviations : 0.11 % 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 aren not related in a simple way. whole: -1.60 (0.18), residues: 1891 helix: -1.05 (0.22), residues: 406 sheet: -0.56 (0.22), residues: 525 loop : -1.28 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 542 TYR 0.037 0.002 TYR B 638 PHE 0.059 0.002 PHE A 376 TRP 0.044 0.002 TRP F 631 HIS 0.024 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00452 (17004) covalent geometry : angle 1.00094 (23084) SS BOND : bond 0.05673 ( 38) SS BOND : angle 4.68166 ( 76) hydrogen bonds : bond 0.22029 ( 566) hydrogen bonds : angle 8.43610 ( 1599) link_ALPHA1-3 : bond 0.01208 ( 5) link_ALPHA1-3 : angle 2.66866 ( 15) link_ALPHA1-6 : bond 0.01031 ( 2) link_ALPHA1-6 : angle 1.31268 ( 6) link_BETA1-4 : bond 0.00678 ( 43) link_BETA1-4 : angle 1.93087 ( 129) link_NAG-ASN : bond 0.00530 ( 59) link_NAG-ASN : angle 3.00287 ( 177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.8385 (tpp) cc_final: 0.8109 (tpp) REVERT: B 648 GLU cc_start: 0.8488 (mp0) cc_final: 0.8229 (pm20) REVERT: F 624 ASP cc_start: 0.8626 (m-30) cc_final: 0.8264 (t0) REVERT: H 65 ASN cc_start: 0.8985 (m-40) cc_final: 0.8624 (p0) REVERT: I 161 MET cc_start: 0.9129 (tpt) cc_final: 0.8826 (tpp) REVERT: I 475 MET cc_start: 0.8379 (tpp) cc_final: 0.7927 (mpp) REVERT: J 577 GLN cc_start: 0.8655 (mt0) cc_final: 0.8276 (mt0) REVERT: L 17 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8037 (mtmm) REVERT: L 79 GLN cc_start: 0.8242 (mm110) cc_final: 0.7671 (mm-40) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.6708 time to fit residues: 124.9842 Evaluate side-chains 138 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0000 chunk 149 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.081340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061088 restraints weight = 43405.304| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.94 r_work: 0.2913 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17151 Z= 0.187 Angle : 0.684 14.172 23487 Z= 0.325 Chirality : 0.046 0.278 2912 Planarity : 0.004 0.037 2791 Dihedral : 7.780 57.033 4316 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.76 % Allowed : 11.74 % Favored : 85.50 % 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 aren not related in a simple way. whole: -0.62 (0.19), residues: 1891 helix: 0.58 (0.26), residues: 395 sheet: -0.38 (0.21), residues: 583 loop : -0.79 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 542 TYR 0.013 0.001 TYR J 638 PHE 0.025 0.002 PHE A 376 TRP 0.015 0.001 TRP J 631 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00430 (17004) covalent geometry : angle 0.63129 (23084) SS BOND : bond 0.00388 ( 38) SS BOND : angle 1.59551 ( 76) hydrogen bonds : bond 0.04835 ( 566) hydrogen bonds : angle 5.85826 ( 1599) link_ALPHA1-3 : bond 0.00898 ( 5) link_ALPHA1-3 : angle 2.27004 ( 15) link_ALPHA1-6 : bond 0.00845 ( 2) link_ALPHA1-6 : angle 1.17710 ( 6) link_BETA1-4 : bond 0.00475 ( 43) link_BETA1-4 : angle 1.78080 ( 129) link_NAG-ASN : bond 0.00323 ( 59) link_NAG-ASN : angle 2.48993 ( 177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8472 (tpp) cc_final: 0.8171 (tpp) REVERT: B 574 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8280 (ptmt) REVERT: B 601 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: E 161 MET cc_start: 0.9042 (tpp) cc_final: 0.8822 (tpt) REVERT: F 530 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6393 (mtt) REVERT: F 657 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8318 (tm-30) REVERT: H 65 ASN cc_start: 0.9092 (m-40) cc_final: 0.8618 (p0) REVERT: I 475 MET cc_start: 0.8393 (tpp) cc_final: 0.7949 (mpp) REVERT: J 535 MET cc_start: 0.8794 (mpt) cc_final: 0.8509 (mpt) REVERT: L 17 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8046 (mtmm) outliers start: 47 outliers final: 17 residues processed: 165 average time/residue: 0.5871 time to fit residues: 107.8865 Evaluate side-chains 146 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain L residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 258 GLN F 543 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058263 restraints weight = 43548.474| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.94 r_work: 0.2845 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17151 Z= 0.207 Angle : 0.663 11.902 23487 Z= 0.316 Chirality : 0.046 0.282 2912 Planarity : 0.004 0.039 2791 Dihedral : 7.580 59.565 4316 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.11 % Allowed : 11.92 % Favored : 84.97 % 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 aren not related in a simple way. whole: -0.32 (0.19), residues: 1891 helix: 0.88 (0.27), residues: 413 sheet: -0.32 (0.21), residues: 587 loop : -0.55 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 16 TYR 0.016 0.001 TYR J 638 PHE 0.021 0.002 PHE A 376 TRP 0.014 0.001 TRP E 69 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00485 (17004) covalent geometry : angle 0.61462 (23084) SS BOND : bond 0.00289 ( 38) SS BOND : angle 1.51926 ( 76) hydrogen bonds : bond 0.04385 ( 566) hydrogen bonds : angle 5.33048 ( 1599) link_ALPHA1-3 : bond 0.00903 ( 5) link_ALPHA1-3 : angle 2.08297 ( 15) link_ALPHA1-6 : bond 0.00951 ( 2) link_ALPHA1-6 : angle 1.58238 ( 6) link_BETA1-4 : bond 0.00415 ( 43) link_BETA1-4 : angle 1.67149 ( 129) link_NAG-ASN : bond 0.00374 ( 59) link_NAG-ASN : angle 2.37565 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8459 (tpp) cc_final: 0.8145 (tpp) REVERT: B 570 VAL cc_start: 0.8116 (t) cc_final: 0.7851 (p) REVERT: B 574 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8227 (ptmt) REVERT: E 475 MET cc_start: 0.8614 (mmm) cc_final: 0.7464 (mpp) REVERT: F 657 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 65 ASN cc_start: 0.9050 (m-40) cc_final: 0.8647 (p0) REVERT: I 67 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8145 (t0) REVERT: I 475 MET cc_start: 0.8338 (tpp) cc_final: 0.7935 (mpp) REVERT: J 588 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: L 13 GLU cc_start: 0.7548 (tp30) cc_final: 0.7184 (tp30) outliers start: 53 outliers final: 20 residues processed: 175 average time/residue: 0.5800 time to fit residues: 113.3294 Evaluate side-chains 149 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 176 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055920 restraints weight = 43616.539| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.91 r_work: 0.2785 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 17151 Z= 0.330 Angle : 0.741 11.331 23487 Z= 0.354 Chirality : 0.048 0.263 2912 Planarity : 0.004 0.037 2791 Dihedral : 7.892 59.991 4316 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.82 % Allowed : 12.86 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.40 (0.19), residues: 1891 helix: 0.94 (0.27), residues: 408 sheet: -0.45 (0.20), residues: 590 loop : -0.60 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 16 TYR 0.015 0.002 TYR F 638 PHE 0.020 0.002 PHE I 383 TRP 0.016 0.002 TRP E 69 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00776 (17004) covalent geometry : angle 0.69422 (23084) SS BOND : bond 0.00414 ( 38) SS BOND : angle 1.69174 ( 76) hydrogen bonds : bond 0.04509 ( 566) hydrogen bonds : angle 5.37336 ( 1599) link_ALPHA1-3 : bond 0.00726 ( 5) link_ALPHA1-3 : angle 2.11298 ( 15) link_ALPHA1-6 : bond 0.00677 ( 2) link_ALPHA1-6 : angle 1.51685 ( 6) link_BETA1-4 : bond 0.00423 ( 43) link_BETA1-4 : angle 1.74358 ( 129) link_NAG-ASN : bond 0.00531 ( 59) link_NAG-ASN : angle 2.47192 ( 177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8456 (tpp) cc_final: 0.8103 (tpp) REVERT: B 570 VAL cc_start: 0.8082 (t) cc_final: 0.7816 (p) REVERT: B 574 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8224 (ptmt) REVERT: B 621 GLU cc_start: 0.8343 (pp20) cc_final: 0.8095 (pm20) REVERT: E 205 CYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7725 (m) REVERT: F 657 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8292 (tm-30) REVERT: H 65 ASN cc_start: 0.9094 (m-40) cc_final: 0.8483 (t0) REVERT: I 475 MET cc_start: 0.8329 (tpp) cc_final: 0.7895 (mpp) REVERT: L 83 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5732 (tp30) outliers start: 65 outliers final: 30 residues processed: 186 average time/residue: 0.5445 time to fit residues: 114.3527 Evaluate side-chains 157 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 140 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 0.0070 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN F 543 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.078330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057759 restraints weight = 43118.011| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.92 r_work: 0.2830 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17151 Z= 0.147 Angle : 0.633 11.677 23487 Z= 0.300 Chirality : 0.045 0.257 2912 Planarity : 0.003 0.035 2791 Dihedral : 7.621 59.064 4316 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.64 % Allowed : 14.86 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.19 (0.19), residues: 1891 helix: 1.21 (0.27), residues: 408 sheet: -0.27 (0.21), residues: 575 loop : -0.56 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 16 TYR 0.010 0.001 TYR A 318 PHE 0.017 0.002 PHE A 376 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00341 (17004) covalent geometry : angle 0.58722 (23084) SS BOND : bond 0.00315 ( 38) SS BOND : angle 1.40832 ( 76) hydrogen bonds : bond 0.03838 ( 566) hydrogen bonds : angle 5.18180 ( 1599) link_ALPHA1-3 : bond 0.00814 ( 5) link_ALPHA1-3 : angle 1.98612 ( 15) link_ALPHA1-6 : bond 0.00837 ( 2) link_ALPHA1-6 : angle 1.43390 ( 6) link_BETA1-4 : bond 0.00401 ( 43) link_BETA1-4 : angle 1.59657 ( 129) link_NAG-ASN : bond 0.00321 ( 59) link_NAG-ASN : angle 2.24964 ( 177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 VAL cc_start: 0.8062 (t) cc_final: 0.7788 (p) REVERT: B 574 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8247 (ptmt) REVERT: E 475 MET cc_start: 0.8508 (mmm) cc_final: 0.7476 (mpp) REVERT: F 657 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8243 (tm-30) REVERT: H 65 ASN cc_start: 0.9067 (m-40) cc_final: 0.8419 (t0) REVERT: I 475 MET cc_start: 0.8333 (tpp) cc_final: 0.7822 (pmm) REVERT: J 535 MET cc_start: 0.8738 (mpt) cc_final: 0.8369 (mpt) REVERT: L 83 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5660 (tp30) outliers start: 45 outliers final: 23 residues processed: 161 average time/residue: 0.5833 time to fit residues: 104.9849 Evaluate side-chains 147 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 118 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 161 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 302 ASN A 428 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058800 restraints weight = 42294.329| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.76 r_work: 0.2867 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17151 Z= 0.118 Angle : 0.609 10.545 23487 Z= 0.287 Chirality : 0.044 0.251 2912 Planarity : 0.003 0.044 2791 Dihedral : 7.242 55.955 4316 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.52 % Allowed : 14.86 % Favored : 82.62 % 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 aren not related in a simple way. whole: -0.04 (0.20), residues: 1891 helix: 1.32 (0.27), residues: 413 sheet: -0.16 (0.21), residues: 571 loop : -0.48 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 16 TYR 0.019 0.001 TYR B 638 PHE 0.016 0.001 PHE A 376 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00268 (17004) covalent geometry : angle 0.56650 (23084) SS BOND : bond 0.00226 ( 38) SS BOND : angle 1.35116 ( 76) hydrogen bonds : bond 0.03512 ( 566) hydrogen bonds : angle 5.00347 ( 1599) link_ALPHA1-3 : bond 0.00783 ( 5) link_ALPHA1-3 : angle 1.90850 ( 15) link_ALPHA1-6 : bond 0.00804 ( 2) link_ALPHA1-6 : angle 1.42990 ( 6) link_BETA1-4 : bond 0.00441 ( 43) link_BETA1-4 : angle 1.54233 ( 129) link_NAG-ASN : bond 0.00300 ( 59) link_NAG-ASN : angle 2.10802 ( 177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 VAL cc_start: 0.8020 (t) cc_final: 0.7749 (p) REVERT: B 657 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8189 (pp20) REVERT: F 655 LYS cc_start: 0.8555 (tptt) cc_final: 0.8256 (tppt) REVERT: F 657 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8214 (tm-30) REVERT: I 475 MET cc_start: 0.8301 (tpp) cc_final: 0.7858 (mpp) REVERT: L 83 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5670 (tp30) outliers start: 43 outliers final: 24 residues processed: 166 average time/residue: 0.6037 time to fit residues: 111.3545 Evaluate side-chains 148 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 74 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.056126 restraints weight = 43097.628| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.89 r_work: 0.2786 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17151 Z= 0.267 Angle : 0.708 11.553 23487 Z= 0.336 Chirality : 0.047 0.269 2912 Planarity : 0.004 0.059 2791 Dihedral : 7.492 59.620 4316 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.94 % Allowed : 15.21 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.22 (0.19), residues: 1891 helix: 1.26 (0.27), residues: 408 sheet: -0.37 (0.21), residues: 575 loop : -0.56 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 16 TYR 0.018 0.002 TYR B 638 PHE 0.024 0.002 PHE A 376 TRP 0.020 0.002 TRP A 112 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00627 (17004) covalent geometry : angle 0.66396 (23084) SS BOND : bond 0.00348 ( 38) SS BOND : angle 1.60517 ( 76) hydrogen bonds : bond 0.04246 ( 566) hydrogen bonds : angle 5.15736 ( 1599) link_ALPHA1-3 : bond 0.00675 ( 5) link_ALPHA1-3 : angle 1.95429 ( 15) link_ALPHA1-6 : bond 0.00553 ( 2) link_ALPHA1-6 : angle 1.48567 ( 6) link_BETA1-4 : bond 0.00375 ( 43) link_BETA1-4 : angle 1.67356 ( 129) link_NAG-ASN : bond 0.00470 ( 59) link_NAG-ASN : angle 2.32231 ( 177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 VAL cc_start: 0.8089 (t) cc_final: 0.7804 (p) REVERT: B 655 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8121 (ptpp) REVERT: E 475 MET cc_start: 0.8624 (mmm) cc_final: 0.7572 (mpp) REVERT: F 657 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8307 (tm-30) REVERT: I 475 MET cc_start: 0.8349 (tpp) cc_final: 0.7830 (pmm) REVERT: L 83 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5756 (tp30) outliers start: 50 outliers final: 31 residues processed: 159 average time/residue: 0.5420 time to fit residues: 96.9132 Evaluate side-chains 157 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 53 optimal weight: 0.4980 chunk 23 optimal weight: 0.0030 chunk 155 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.079779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.059301 restraints weight = 42867.915| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.92 r_work: 0.2867 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17151 Z= 0.106 Angle : 0.611 9.829 23487 Z= 0.288 Chirality : 0.043 0.249 2912 Planarity : 0.003 0.045 2791 Dihedral : 7.070 55.669 4316 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 16.15 % Favored : 81.68 % 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 aren not related in a simple way. whole: 0.04 (0.20), residues: 1891 helix: 1.60 (0.27), residues: 401 sheet: -0.16 (0.21), residues: 563 loop : -0.48 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 16 TYR 0.009 0.001 TYR I 484 PHE 0.014 0.001 PHE A 376 TRP 0.019 0.001 TRP J 631 HIS 0.002 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00234 (17004) covalent geometry : angle 0.57179 (23084) SS BOND : bond 0.00219 ( 38) SS BOND : angle 1.30737 ( 76) hydrogen bonds : bond 0.03373 ( 566) hydrogen bonds : angle 4.91438 ( 1599) link_ALPHA1-3 : bond 0.00693 ( 5) link_ALPHA1-3 : angle 1.89637 ( 15) link_ALPHA1-6 : bond 0.00786 ( 2) link_ALPHA1-6 : angle 1.34135 ( 6) link_BETA1-4 : bond 0.00471 ( 43) link_BETA1-4 : angle 1.49949 ( 129) link_NAG-ASN : bond 0.00305 ( 59) link_NAG-ASN : angle 2.03241 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 VAL cc_start: 0.7978 (t) cc_final: 0.7701 (p) REVERT: E 475 MET cc_start: 0.8494 (mmm) cc_final: 0.7439 (mpp) REVERT: F 535 MET cc_start: 0.9084 (mpp) cc_final: 0.8864 (mmt) REVERT: F 655 LYS cc_start: 0.8568 (tptt) cc_final: 0.8177 (mmmt) REVERT: F 657 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8228 (tm-30) REVERT: I 475 MET cc_start: 0.8238 (tpp) cc_final: 0.7759 (pmm) REVERT: L 83 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5654 (tp30) outliers start: 37 outliers final: 21 residues processed: 155 average time/residue: 0.5472 time to fit residues: 95.0507 Evaluate side-chains 143 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 148 optimal weight: 0.2980 chunk 40 optimal weight: 0.0570 chunk 172 optimal weight: 6.9990 chunk 187 optimal weight: 0.0170 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.059519 restraints weight = 42891.115| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.93 r_work: 0.2871 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17151 Z= 0.107 Angle : 0.613 11.901 23487 Z= 0.287 Chirality : 0.043 0.229 2912 Planarity : 0.003 0.048 2791 Dihedral : 6.847 55.401 4316 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.88 % Allowed : 16.56 % Favored : 81.56 % 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 aren not related in a simple way. whole: 0.16 (0.20), residues: 1891 helix: 1.73 (0.27), residues: 400 sheet: -0.07 (0.21), residues: 563 loop : -0.43 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 16 TYR 0.036 0.001 TYR J 638 PHE 0.017 0.001 PHE A 376 TRP 0.016 0.001 TRP J 631 HIS 0.003 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00242 (17004) covalent geometry : angle 0.57245 (23084) SS BOND : bond 0.00204 ( 38) SS BOND : angle 1.27281 ( 76) hydrogen bonds : bond 0.03297 ( 566) hydrogen bonds : angle 4.81918 ( 1599) link_ALPHA1-3 : bond 0.00647 ( 5) link_ALPHA1-3 : angle 1.86859 ( 15) link_ALPHA1-6 : bond 0.00730 ( 2) link_ALPHA1-6 : angle 1.40988 ( 6) link_BETA1-4 : bond 0.00437 ( 43) link_BETA1-4 : angle 1.49910 ( 129) link_NAG-ASN : bond 0.00273 ( 59) link_NAG-ASN : angle 2.10407 ( 177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 VAL cc_start: 0.7989 (t) cc_final: 0.7686 (p) REVERT: B 657 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8311 (tm-30) REVERT: E 475 MET cc_start: 0.8504 (mmm) cc_final: 0.7473 (mpp) REVERT: F 530 MET cc_start: 0.7859 (mtt) cc_final: 0.7606 (mtt) REVERT: F 655 LYS cc_start: 0.8522 (tptt) cc_final: 0.8297 (tppt) REVERT: F 657 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8308 (tm-30) REVERT: I 475 MET cc_start: 0.8285 (tpp) cc_final: 0.7780 (pmm) REVERT: L 83 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5575 (tp30) outliers start: 32 outliers final: 25 residues processed: 149 average time/residue: 0.5929 time to fit residues: 98.2448 Evaluate side-chains 150 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058363 restraints weight = 43009.140| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.92 r_work: 0.2845 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17151 Z= 0.149 Angle : 0.636 11.336 23487 Z= 0.300 Chirality : 0.044 0.258 2912 Planarity : 0.003 0.046 2791 Dihedral : 6.904 56.905 4316 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 16.62 % Favored : 81.50 % 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 aren not related in a simple way. whole: 0.16 (0.20), residues: 1891 helix: 1.77 (0.27), residues: 395 sheet: -0.05 (0.21), residues: 559 loop : -0.45 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 16 TYR 0.060 0.001 TYR J 638 PHE 0.016 0.001 PHE I 376 TRP 0.019 0.001 TRP J 631 HIS 0.003 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00348 (17004) covalent geometry : angle 0.59595 (23084) SS BOND : bond 0.00266 ( 38) SS BOND : angle 1.37108 ( 76) hydrogen bonds : bond 0.03511 ( 566) hydrogen bonds : angle 4.85046 ( 1599) link_ALPHA1-3 : bond 0.00597 ( 5) link_ALPHA1-3 : angle 1.86911 ( 15) link_ALPHA1-6 : bond 0.00641 ( 2) link_ALPHA1-6 : angle 1.39111 ( 6) link_BETA1-4 : bond 0.00399 ( 43) link_BETA1-4 : angle 1.51420 ( 129) link_NAG-ASN : bond 0.00280 ( 59) link_NAG-ASN : angle 2.12690 ( 177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7195 (tptt) REVERT: B 570 VAL cc_start: 0.8047 (t) cc_final: 0.7735 (p) REVERT: B 657 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8369 (tm-30) REVERT: E 475 MET cc_start: 0.8554 (mmm) cc_final: 0.7461 (mpp) REVERT: F 655 LYS cc_start: 0.8528 (tptt) cc_final: 0.8307 (tppt) REVERT: F 657 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8315 (tm-30) REVERT: I 475 MET cc_start: 0.8283 (tpp) cc_final: 0.7780 (pmm) REVERT: L 83 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5649 (tp30) outliers start: 32 outliers final: 22 residues processed: 146 average time/residue: 0.6114 time to fit residues: 99.5225 Evaluate side-chains 144 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.077836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058035 restraints weight = 42195.212| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.77 r_work: 0.2846 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17151 Z= 0.150 Angle : 0.637 11.292 23487 Z= 0.302 Chirality : 0.044 0.251 2912 Planarity : 0.003 0.044 2791 Dihedral : 6.899 56.898 4316 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.82 % Allowed : 16.74 % Favored : 81.44 % 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 aren not related in a simple way. whole: 0.19 (0.20), residues: 1891 helix: 1.78 (0.27), residues: 396 sheet: -0.05 (0.21), residues: 559 loop : -0.41 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 16 TYR 0.050 0.001 TYR J 638 PHE 0.017 0.001 PHE I 376 TRP 0.014 0.001 TRP E 479 HIS 0.003 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00352 (17004) covalent geometry : angle 0.59779 (23084) SS BOND : bond 0.00264 ( 38) SS BOND : angle 1.37402 ( 76) hydrogen bonds : bond 0.03509 ( 566) hydrogen bonds : angle 4.85431 ( 1599) link_ALPHA1-3 : bond 0.00585 ( 5) link_ALPHA1-3 : angle 1.87191 ( 15) link_ALPHA1-6 : bond 0.00636 ( 2) link_ALPHA1-6 : angle 1.38004 ( 6) link_BETA1-4 : bond 0.00401 ( 43) link_BETA1-4 : angle 1.50345 ( 129) link_NAG-ASN : bond 0.00291 ( 59) link_NAG-ASN : angle 2.10779 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4351.93 seconds wall clock time: 75 minutes 25.61 seconds (4525.61 seconds total)