Starting phenix.real_space_refine on Sun Jun 15 02:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btl_44893/06_2025/9btl_44893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btl_44893/06_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_44893/06_2025/9btl_44893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btl_44893/06_2025/9btl_44893.map" model { file = "/net/cci-nas-00/data/ceres_data/9btl_44893/06_2025/9btl_44893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btl_44893/06_2025/9btl_44893.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.02, per 1000 atoms: 0.60 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: 5.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.25 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: 5.72 Time building geometry restraints manager: 6.41 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 505 or resid 601 throu \ gh 605)) selection = (chain 'E' and (resid 33 through 185 or resid 189 through 505 or resid 601 throu \ gh 605)) selection = (chain 'I' and (resid 33 through 185 or resid 189 through 397 or resid 412 throu \ gh 505 or resid 601 through 605)) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 520 through 664 or resid 701)) selection = (chain 'J' and (resid 520 through 545 or resid 568 through 664 or resid 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: 2.370 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: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.190 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.300 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:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.044 0.002 TRP F 631 HIS 0.024 0.002 HIS A 374 PHE 0.059 0.002 PHE A 376 TYR 0.037 0.002 TYR B 638 ARG 0.015 0.001 ARG J 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 59) link_NAG-ASN : angle 3.00287 ( 177) 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_ALPHA1-3 : bond 0.01208 ( 5) link_ALPHA1-3 : angle 2.66866 ( 15) hydrogen bonds : bond 0.22029 ( 566) hydrogen bonds : angle 8.43610 ( 1599) SS BOND : bond 0.05673 ( 38) SS BOND : angle 4.68166 ( 76) covalent geometry : bond 0.00452 (17004) covalent geometry : angle 1.00094 (23084) *********************** 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 : 2.002 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: 0.8290 (pt0) 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: 0.7672 (mm-40) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 1.3812 time to fit residues: 258.1113 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 : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.082956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062945 restraints weight = 42970.813| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.93 r_work: 0.2959 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17151 Z= 0.145 Angle : 0.664 14.674 23487 Z= 0.316 Chirality : 0.045 0.286 2912 Planarity : 0.004 0.038 2791 Dihedral : 7.683 56.551 4316 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 11.69 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1891 helix: 0.55 (0.26), residues: 395 sheet: -0.34 (0.21), residues: 580 loop : -0.81 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 631 HIS 0.006 0.001 HIS A 374 PHE 0.022 0.002 PHE A 376 TYR 0.022 0.001 TYR F 638 ARG 0.006 0.000 ARG J 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 59) link_NAG-ASN : angle 2.46805 ( 177) link_ALPHA1-6 : bond 0.00880 ( 2) link_ALPHA1-6 : angle 1.16027 ( 6) link_BETA1-4 : bond 0.00513 ( 43) link_BETA1-4 : angle 1.76457 ( 129) link_ALPHA1-3 : bond 0.00973 ( 5) link_ALPHA1-3 : angle 2.29075 ( 15) hydrogen bonds : bond 0.05047 ( 566) hydrogen bonds : angle 6.00444 ( 1599) SS BOND : bond 0.00248 ( 38) SS BOND : angle 1.53108 ( 76) covalent geometry : bond 0.00328 (17004) covalent geometry : angle 0.61105 (23084) *********************** 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 187 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8435 (tpp) cc_final: 0.8133 (tpp) REVERT: B 601 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: F 530 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6038 (mtt) REVERT: F 657 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8354 (tm-30) REVERT: H 1 GLN cc_start: 0.7750 (tt0) cc_final: 0.7511 (tt0) REVERT: H 65 ASN cc_start: 0.9068 (m-40) cc_final: 0.8597 (p0) REVERT: I 426 MET cc_start: 0.6373 (pmm) cc_final: 0.6165 (ptm) REVERT: I 475 MET cc_start: 0.8409 (tpp) cc_final: 0.7960 (mpp) REVERT: J 535 MET cc_start: 0.8775 (mpt) cc_final: 0.8565 (mpt) REVERT: L 17 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8049 (mtmm) outliers start: 47 outliers final: 15 residues processed: 168 average time/residue: 1.2974 time to fit residues: 244.1544 Evaluate side-chains 145 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 277 ILE Chi-restraints excluded: chain E residue 309 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 20 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 0.0470 chunk 58 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS F 543 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065025 restraints weight = 42152.390| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.71 r_work: 0.2961 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17151 Z= 0.113 Angle : 0.594 12.306 23487 Z= 0.280 Chirality : 0.044 0.280 2912 Planarity : 0.003 0.036 2791 Dihedral : 7.262 55.248 4316 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.52 % Allowed : 12.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 1891 helix: 1.25 (0.27), residues: 395 sheet: -0.13 (0.21), residues: 573 loop : -0.61 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS I 105 PHE 0.017 0.001 PHE A 376 TYR 0.015 0.001 TYR J 638 ARG 0.005 0.000 ARG L 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 59) link_NAG-ASN : angle 2.22594 ( 177) link_ALPHA1-6 : bond 0.01041 ( 2) link_ALPHA1-6 : angle 1.51353 ( 6) link_BETA1-4 : bond 0.00485 ( 43) link_BETA1-4 : angle 1.62205 ( 129) link_ALPHA1-3 : bond 0.00988 ( 5) link_ALPHA1-3 : angle 2.07497 ( 15) hydrogen bonds : bond 0.03900 ( 566) hydrogen bonds : angle 5.34371 ( 1599) SS BOND : bond 0.00205 ( 38) SS BOND : angle 1.29801 ( 76) covalent geometry : bond 0.00250 (17004) covalent geometry : angle 0.54502 (23084) *********************** 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 179 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8406 (tpp) cc_final: 0.8131 (tpp) REVERT: B 570 VAL cc_start: 0.8058 (t) cc_final: 0.7791 (p) REVERT: F 657 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8258 (tm-30) REVERT: H 4 LEU cc_start: 0.7732 (mp) cc_final: 0.7251 (mt) REVERT: H 65 ASN cc_start: 0.9015 (m-40) cc_final: 0.8444 (t0) REVERT: I 475 MET cc_start: 0.8426 (tpp) cc_final: 0.7986 (mpp) REVERT: J 535 MET cc_start: 0.8819 (mpt) cc_final: 0.8389 (mpt) REVERT: J 588 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7608 (ttm-80) REVERT: L 17 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8070 (mtmm) outliers start: 43 outliers final: 17 residues processed: 160 average time/residue: 1.3297 time to fit residues: 237.1311 Evaluate side-chains 145 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 633 LYS Chi-restraints excluded: chain E residue 277 ILE 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 36 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 625 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain L residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 16 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.082273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061997 restraints weight = 42842.291| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.95 r_work: 0.2933 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17151 Z= 0.118 Angle : 0.584 11.325 23487 Z= 0.275 Chirality : 0.043 0.268 2912 Planarity : 0.003 0.032 2791 Dihedral : 7.142 55.367 4316 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.58 % Allowed : 12.80 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1891 helix: 1.53 (0.28), residues: 395 sheet: -0.03 (0.21), residues: 573 loop : -0.50 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.003 0.001 HIS E 374 PHE 0.015 0.001 PHE A 376 TYR 0.012 0.001 TYR B 638 ARG 0.003 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 59) link_NAG-ASN : angle 2.13138 ( 177) link_ALPHA1-6 : bond 0.00918 ( 2) link_ALPHA1-6 : angle 1.47534 ( 6) link_BETA1-4 : bond 0.00454 ( 43) link_BETA1-4 : angle 1.57049 ( 129) link_ALPHA1-3 : bond 0.00957 ( 5) link_ALPHA1-3 : angle 2.01665 ( 15) hydrogen bonds : bond 0.03556 ( 566) hydrogen bonds : angle 5.09258 ( 1599) SS BOND : bond 0.00343 ( 38) SS BOND : angle 1.14748 ( 76) covalent geometry : bond 0.00268 (17004) covalent geometry : angle 0.53946 (23084) *********************** 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 174 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8401 (tpp) cc_final: 0.8133 (tpp) REVERT: B 570 VAL cc_start: 0.8082 (t) cc_final: 0.7786 (p) REVERT: E 205 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7808 (m) REVERT: F 624 ASP cc_start: 0.8544 (m-30) cc_final: 0.8290 (t0) REVERT: F 657 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8258 (tm-30) REVERT: H 65 ASN cc_start: 0.9005 (m-40) cc_final: 0.8429 (t0) REVERT: I 475 MET cc_start: 0.8445 (tpp) cc_final: 0.8006 (mpp) REVERT: J 535 MET cc_start: 0.8839 (mpt) cc_final: 0.8340 (mpt) REVERT: L 78 LEU cc_start: 0.8219 (tt) cc_final: 0.7955 (tt) REVERT: L 83 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5730 (tp30) outliers start: 44 outliers final: 18 residues processed: 159 average time/residue: 1.2993 time to fit residues: 230.6883 Evaluate side-chains 146 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 331 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain F residue 599 SER 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 36 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 125 optimal weight: 0.0050 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 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 = 0.3421 r_free = 0.3421 target = 0.078062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057198 restraints weight = 43806.647| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.96 r_work: 0.2816 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17151 Z= 0.264 Angle : 0.709 12.897 23487 Z= 0.339 Chirality : 0.047 0.259 2912 Planarity : 0.004 0.038 2791 Dihedral : 7.550 59.916 4316 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.05 % Allowed : 12.80 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1891 helix: 1.36 (0.28), residues: 401 sheet: -0.20 (0.21), residues: 575 loop : -0.58 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.006 0.001 HIS E 374 PHE 0.023 0.002 PHE I 383 TYR 0.014 0.001 TYR F 638 ARG 0.010 0.001 ARG L 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 59) link_NAG-ASN : angle 2.33948 ( 177) link_ALPHA1-6 : bond 0.00622 ( 2) link_ALPHA1-6 : angle 1.48065 ( 6) link_BETA1-4 : bond 0.00396 ( 43) link_BETA1-4 : angle 1.68697 ( 129) link_ALPHA1-3 : bond 0.00806 ( 5) link_ALPHA1-3 : angle 2.01910 ( 15) hydrogen bonds : bond 0.04268 ( 566) hydrogen bonds : angle 5.16644 ( 1599) SS BOND : bond 0.00338 ( 38) SS BOND : angle 1.58644 ( 76) covalent geometry : bond 0.00619 (17004) covalent geometry : angle 0.66497 (23084) *********************** 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 182 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9264 (ttt) cc_final: 0.9053 (ttt) REVERT: A 376 PHE cc_start: 0.7822 (m-10) cc_final: 0.7575 (m-10) REVERT: A 475 MET cc_start: 0.8469 (tpp) cc_final: 0.8122 (tpp) REVERT: B 570 VAL cc_start: 0.8073 (t) cc_final: 0.7772 (p) REVERT: E 475 MET cc_start: 0.8613 (mmm) cc_final: 0.7568 (mpp) REVERT: F 657 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 5 GLN cc_start: 0.8984 (mt0) cc_final: 0.8579 (mp10) REVERT: H 13 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8107 (mmmt) REVERT: H 65 ASN cc_start: 0.9072 (m-40) cc_final: 0.8450 (t0) REVERT: I 475 MET cc_start: 0.8395 (tpp) cc_final: 0.7938 (mpp) REVERT: J 535 MET cc_start: 0.8830 (mpt) cc_final: 0.8427 (mpt) REVERT: L 78 LEU cc_start: 0.8332 (tt) cc_final: 0.8072 (tt) REVERT: L 83 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5732 (tp30) REVERT: L 103 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7965 (tpp-160) outliers start: 52 outliers final: 24 residues processed: 165 average time/residue: 1.2173 time to fit residues: 225.9277 Evaluate side-chains 150 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 277 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain E residue 205 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 80 LEU Chi-restraints excluded: chain H residue 107 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 5 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 177 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.0040 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 67 ASN J 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059596 restraints weight = 42854.083| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.92 r_work: 0.2877 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17151 Z= 0.116 Angle : 0.598 10.599 23487 Z= 0.283 Chirality : 0.043 0.250 2912 Planarity : 0.003 0.031 2791 Dihedral : 7.240 57.456 4316 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.29 % Allowed : 14.50 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1891 helix: 1.56 (0.28), residues: 401 sheet: -0.05 (0.21), residues: 570 loop : -0.47 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS I 105 PHE 0.020 0.001 PHE A 376 TYR 0.016 0.001 TYR B 638 ARG 0.005 0.000 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 59) link_NAG-ASN : angle 2.09403 ( 177) link_ALPHA1-6 : bond 0.00815 ( 2) link_ALPHA1-6 : angle 1.38594 ( 6) link_BETA1-4 : bond 0.00431 ( 43) link_BETA1-4 : angle 1.52616 ( 129) link_ALPHA1-3 : bond 0.00793 ( 5) link_ALPHA1-3 : angle 1.91865 ( 15) hydrogen bonds : bond 0.03493 ( 566) hydrogen bonds : angle 4.99278 ( 1599) SS BOND : bond 0.00303 ( 38) SS BOND : angle 1.31810 ( 76) covalent geometry : bond 0.00261 (17004) covalent geometry : angle 0.55517 (23084) *********************** 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 173 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9277 (ttt) cc_final: 0.9070 (ttt) REVERT: A 475 MET cc_start: 0.8442 (tpp) cc_final: 0.8085 (tpp) REVERT: B 570 VAL cc_start: 0.7985 (t) cc_final: 0.7700 (p) REVERT: F 657 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8272 (tm-30) REVERT: H 5 GLN cc_start: 0.8997 (mt0) cc_final: 0.8597 (mp10) REVERT: H 13 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8025 (mmmt) REVERT: I 475 MET cc_start: 0.8315 (tpp) cc_final: 0.7909 (mpp) REVERT: L 78 LEU cc_start: 0.8288 (tt) cc_final: 0.7994 (tt) REVERT: L 83 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5786 (tp30) REVERT: L 103 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7884 (tpp-160) outliers start: 39 outliers final: 19 residues processed: 159 average time/residue: 1.2919 time to fit residues: 229.5868 Evaluate side-chains 147 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 277 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 636 SER 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 H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL 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 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 79 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.057800 restraints weight = 43189.741| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.94 r_work: 0.2830 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.005 0.051 17151 Z= 0.194 Angle : 0.648 11.022 23487 Z= 0.308 Chirality : 0.045 0.245 2912 Planarity : 0.003 0.034 2791 Dihedral : 7.247 58.493 4316 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.29 % Allowed : 14.62 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1891 helix: 1.54 (0.27), residues: 402 sheet: -0.12 (0.21), residues: 565 loop : -0.49 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP J 631 HIS 0.005 0.001 HIS E 374 PHE 0.017 0.002 PHE I 383 TYR 0.011 0.001 TYR J 638 ARG 0.007 0.000 ARG L 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 59) link_NAG-ASN : angle 2.15570 ( 177) link_ALPHA1-6 : bond 0.00591 ( 2) link_ALPHA1-6 : angle 1.44642 ( 6) link_BETA1-4 : bond 0.00401 ( 43) link_BETA1-4 : angle 1.59671 ( 129) link_ALPHA1-3 : bond 0.00689 ( 5) link_ALPHA1-3 : angle 1.88390 ( 15) hydrogen bonds : bond 0.03818 ( 566) hydrogen bonds : angle 5.00809 ( 1599) SS BOND : bond 0.00316 ( 38) SS BOND : angle 1.51910 ( 76) covalent geometry : bond 0.00455 (17004) covalent geometry : angle 0.60566 (23084) *********************** 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 169 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9294 (ttt) cc_final: 0.9079 (ttt) REVERT: A 475 MET cc_start: 0.8555 (tpp) cc_final: 0.8220 (tpp) REVERT: B 570 VAL cc_start: 0.8073 (t) cc_final: 0.7761 (p) REVERT: E 475 MET cc_start: 0.8593 (mmm) cc_final: 0.7492 (mpp) REVERT: F 657 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8278 (tm-30) REVERT: H 13 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8019 (mmmt) REVERT: I 475 MET cc_start: 0.8353 (tpp) cc_final: 0.7919 (mpp) REVERT: J 535 MET cc_start: 0.8733 (mpt) cc_final: 0.8343 (mpt) REVERT: L 16 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7938 (tpp-160) REVERT: L 78 LEU cc_start: 0.8220 (tt) cc_final: 0.7909 (tt) REVERT: L 83 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5659 (tp30) outliers start: 39 outliers final: 23 residues processed: 158 average time/residue: 1.2315 time to fit residues: 219.4191 Evaluate side-chains 148 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 277 ILE Chi-restraints excluded: chain A residue 331 CYS 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 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 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 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 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 184 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 428 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057869 restraints weight = 43043.558| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.92 r_work: 0.2834 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17151 Z= 0.177 Angle : 0.631 10.796 23487 Z= 0.301 Chirality : 0.044 0.236 2912 Planarity : 0.003 0.033 2791 Dihedral : 7.183 58.217 4316 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.17 % Allowed : 15.09 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1891 helix: 1.55 (0.27), residues: 402 sheet: -0.07 (0.21), residues: 561 loop : -0.48 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP J 631 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE I 383 TYR 0.017 0.001 TYR B 638 ARG 0.004 0.000 ARG L 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 59) link_NAG-ASN : angle 2.11300 ( 177) link_ALPHA1-6 : bond 0.00657 ( 2) link_ALPHA1-6 : angle 1.38212 ( 6) link_BETA1-4 : bond 0.00399 ( 43) link_BETA1-4 : angle 1.55172 ( 129) link_ALPHA1-3 : bond 0.00655 ( 5) link_ALPHA1-3 : angle 1.89975 ( 15) hydrogen bonds : bond 0.03707 ( 566) hydrogen bonds : angle 4.97890 ( 1599) SS BOND : bond 0.00266 ( 38) SS BOND : angle 1.44519 ( 76) covalent geometry : bond 0.00417 (17004) covalent geometry : angle 0.58943 (23084) *********************** 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 167 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9299 (ttt) cc_final: 0.9087 (ttt) REVERT: A 475 MET cc_start: 0.8515 (tpp) cc_final: 0.8159 (tpp) REVERT: B 570 VAL cc_start: 0.8086 (t) cc_final: 0.7773 (p) REVERT: E 475 MET cc_start: 0.8530 (mmm) cc_final: 0.7484 (mpp) REVERT: F 542 ARG cc_start: 0.8954 (mtp180) cc_final: 0.8675 (mtp180) REVERT: F 657 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8268 (tm-30) REVERT: H 13 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7982 (mmmt) REVERT: I 475 MET cc_start: 0.8302 (tpp) cc_final: 0.7811 (pmm) REVERT: J 535 MET cc_start: 0.8722 (mpt) cc_final: 0.8475 (mpt) REVERT: J 647 GLU cc_start: 0.8083 (tt0) cc_final: 0.7882 (tt0) REVERT: L 78 LEU cc_start: 0.8221 (tt) cc_final: 0.7906 (tt) REVERT: L 83 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5792 (tp30) outliers start: 37 outliers final: 24 residues processed: 155 average time/residue: 1.2410 time to fit residues: 216.1462 Evaluate side-chains 151 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 277 ILE 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 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 H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058834 restraints weight = 42392.797| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.77 r_work: 0.2868 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17151 Z= 0.123 Angle : 0.615 11.529 23487 Z= 0.293 Chirality : 0.044 0.237 2912 Planarity : 0.003 0.056 2791 Dihedral : 6.982 56.375 4316 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.82 % Allowed : 15.50 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1891 helix: 1.63 (0.27), residues: 402 sheet: 0.03 (0.21), residues: 561 loop : -0.44 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 631 HIS 0.003 0.001 HIS I 105 PHE 0.014 0.001 PHE I 376 TYR 0.034 0.001 TYR J 638 ARG 0.018 0.000 ARG L 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 59) link_NAG-ASN : angle 2.12175 ( 177) link_ALPHA1-6 : bond 0.00700 ( 2) link_ALPHA1-6 : angle 1.38412 ( 6) link_BETA1-4 : bond 0.00423 ( 43) link_BETA1-4 : angle 1.50573 ( 129) link_ALPHA1-3 : bond 0.00631 ( 5) link_ALPHA1-3 : angle 1.87475 ( 15) hydrogen bonds : bond 0.03474 ( 566) hydrogen bonds : angle 4.87487 ( 1599) SS BOND : bond 0.00218 ( 38) SS BOND : angle 1.30799 ( 76) covalent geometry : bond 0.00282 (17004) covalent geometry : angle 0.57402 (23084) *********************** 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 156 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9279 (ttt) cc_final: 0.9055 (ttt) REVERT: A 475 MET cc_start: 0.8513 (tpp) cc_final: 0.8131 (tpp) REVERT: B 570 VAL cc_start: 0.8064 (t) cc_final: 0.7748 (p) REVERT: E 475 MET cc_start: 0.8574 (mmm) cc_final: 0.7442 (mpp) REVERT: F 657 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8234 (tm-30) REVERT: H 13 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7923 (mmmt) REVERT: I 475 MET cc_start: 0.8274 (tpp) cc_final: 0.7785 (pmm) REVERT: J 535 MET cc_start: 0.8680 (mpt) cc_final: 0.8284 (mpt) REVERT: L 78 LEU cc_start: 0.8103 (tt) cc_final: 0.7842 (tt) REVERT: L 83 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5733 (tp30) outliers start: 31 outliers final: 22 residues processed: 147 average time/residue: 1.3170 time to fit residues: 219.5099 Evaluate side-chains 143 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 277 ILE Chi-restraints excluded: chain A residue 331 CYS 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 F residue 625 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 3 optimal weight: 0.6980 chunk 128 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 49 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059937 restraints weight = 42502.275| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.78 r_work: 0.2897 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17151 Z= 0.104 Angle : 0.591 11.223 23487 Z= 0.281 Chirality : 0.043 0.276 2912 Planarity : 0.003 0.058 2791 Dihedral : 6.753 55.069 4316 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.41 % Allowed : 16.09 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1891 helix: 1.63 (0.27), residues: 406 sheet: 0.12 (0.21), residues: 554 loop : -0.40 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 631 HIS 0.003 0.000 HIS I 105 PHE 0.015 0.001 PHE I 376 TYR 0.064 0.001 TYR J 638 ARG 0.014 0.000 ARG L 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 59) link_NAG-ASN : angle 2.01362 ( 177) link_ALPHA1-6 : bond 0.00716 ( 2) link_ALPHA1-6 : angle 1.36776 ( 6) link_BETA1-4 : bond 0.00451 ( 43) link_BETA1-4 : angle 1.46061 ( 129) link_ALPHA1-3 : bond 0.00626 ( 5) link_ALPHA1-3 : angle 1.86665 ( 15) hydrogen bonds : bond 0.03239 ( 566) hydrogen bonds : angle 4.74471 ( 1599) SS BOND : bond 0.00202 ( 38) SS BOND : angle 1.21630 ( 76) covalent geometry : bond 0.00234 (17004) covalent geometry : angle 0.55231 (23084) ********************** 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 153 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 VAL cc_start: 0.8037 (t) cc_final: 0.7717 (p) REVERT: B 657 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8342 (tm-30) REVERT: E 475 MET cc_start: 0.8511 (mmm) cc_final: 0.7441 (mpp) REVERT: F 657 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8265 (tm-30) REVERT: H 13 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7900 (mmmt) REVERT: I 475 MET cc_start: 0.8312 (tpp) cc_final: 0.7831 (pmm) REVERT: J 535 MET cc_start: 0.8763 (mpt) cc_final: 0.8480 (mpt) REVERT: L 78 LEU cc_start: 0.8107 (tt) cc_final: 0.7835 (tt) REVERT: L 83 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5693 (tp30) outliers start: 24 outliers final: 18 residues processed: 147 average time/residue: 1.3276 time to fit residues: 218.2852 Evaluate side-chains 142 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 277 ILE Chi-restraints excluded: chain A residue 331 CYS 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 F residue 641 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 539 VAL 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 6 optimal weight: 2.9990 chunk 130 optimal weight: 0.0040 chunk 83 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN J 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.080472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.060125 restraints weight = 42925.259| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.92 r_work: 0.2890 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17151 Z= 0.112 Angle : 0.598 11.106 23487 Z= 0.284 Chirality : 0.043 0.269 2912 Planarity : 0.003 0.055 2791 Dihedral : 6.701 55.276 4316 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.41 % Allowed : 16.27 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1891 helix: 1.63 (0.27), residues: 406 sheet: 0.15 (0.21), residues: 554 loop : -0.38 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 631 HIS 0.003 0.000 HIS I 105 PHE 0.020 0.001 PHE I 376 TYR 0.049 0.001 TYR J 638 ARG 0.014 0.000 ARG L 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 59) link_NAG-ASN : angle 2.00131 ( 177) link_ALPHA1-6 : bond 0.00682 ( 2) link_ALPHA1-6 : angle 1.37525 ( 6) link_BETA1-4 : bond 0.00436 ( 43) link_BETA1-4 : angle 1.45863 ( 129) link_ALPHA1-3 : bond 0.00601 ( 5) link_ALPHA1-3 : angle 1.85800 ( 15) hydrogen bonds : bond 0.03206 ( 566) hydrogen bonds : angle 4.71794 ( 1599) SS BOND : bond 0.00215 ( 38) SS BOND : angle 1.23029 ( 76) covalent geometry : bond 0.00256 (17004) covalent geometry : angle 0.56015 (23084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9199.84 seconds wall clock time: 158 minutes 12.42 seconds (9492.42 seconds total)