Starting phenix.real_space_refine on Sat Mar 7 09:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7llk_23424/03_2026/7llk_23424_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7llk_23424/03_2026/7llk_23424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7llk_23424/03_2026/7llk_23424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7llk_23424/03_2026/7llk_23424.map" model { file = "/net/cci-nas-00/data/ceres_data/7llk_23424/03_2026/7llk_23424_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7llk_23424/03_2026/7llk_23424_trim.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.111 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: 5 Type Number sf(0) Gaussians S 123 5.16 5 C 12739 2.51 5 N 3404 2.21 5 O 4089 1.98 5 H 18627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38982 Number of models: 1 Model: "" Number of chains: 47 Chain: "E" Number of atoms: 6894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6894 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2005 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2100 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "H" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1525 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 6894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6894 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2005 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2100 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1525 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "I" Number of atoms: 6894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6894 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "J" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2005 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "K" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2100 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "L" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1525 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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: 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: "Q" 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: "R" 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: "S" 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 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: "Z" 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 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: "e" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: "j" 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: "k" 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: "l" 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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 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: "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: 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: "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: 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: "s" 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.88, per 1000 atoms: 0.18 Number of scatterers: 38982 At special positions: 0 Unit cell: (159.104, 166.108, 121.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 O 4089 8.00 N 3404 7.00 C 12739 6.00 H 18627 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 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=2.08 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.08 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 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=2.05 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=2.07 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 ALPHA1-6 " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " " BMA c 3 " - " MAN c 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 363 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 88 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 363 " " NAG E 603 " - " ASN E 448 " " NAG I 601 " - " ASN I 133 " " NAG I 602 " - " ASN I 363 " " NAG I 603 " - " ASN I 448 " " NAG M 1 " - " ASN E 88 " " NAG N 1 " - " ASN I 88 " " NAG O 1 " - " ASN E 160 " " NAG Q 1 " - " ASN E 234 " " NAG R 1 " - " ASN E 392 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 301 " " NAG U 1 " - " ASN E 156 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 465 " " NAG Y 1 " - " ASN A 160 " " NAG a 1 " - " ASN A 234 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 301 " " NAG e 1 " - " ASN A 156 " " NAG f 1 " - " ASN A 197 " " NAG g 1 " - " ASN A 465 " " NAG j 1 " - " ASN I 160 " " NAG l 1 " - " ASN I 234 " " NAG m 1 " - " ASN I 392 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 301 " " NAG p 1 " - " ASN I 156 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 465 " Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 49 sheets defined 21.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 334 through 354 removed outlier: 4.135A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.854A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 5.355A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.651A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 646 removed outlier: 6.298A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 653 Processing helix chain 'F' and resid 654 through 663 removed outlier: 4.840A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.854A pdb=" N GLY G 65 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG G 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 77 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.567A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 4.007A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.094A pdb=" N TRP A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.797A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 5.214A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 546 removed outlier: 3.786A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 646 removed outlier: 5.938A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 663 removed outlier: 4.910A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.481A pdb=" N ARG C 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 205 through 209 removed outlier: 3.517A pdb=" N SER I 209 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.155A pdb=" N TRP I 338 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.821A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 484 removed outlier: 5.295A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 546 removed outlier: 3.788A pdb=" N LEU J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 646 removed outlier: 3.509A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN J 640 " --> pdb=" O ASN J 636 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU J 641 " --> pdb=" O ASN J 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 653 Processing helix chain 'J' and resid 654 through 663 removed outlier: 4.764A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 661 " --> pdb=" O GLU J 657 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.803A pdb=" N GLY K 65 " --> pdb=" O SER K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 74 through 77 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 3.736A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.209A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'E' and resid 129 through 132 Processing sheet with id=AA7, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY E 451 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N GLN E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 303 through 308 Processing sheet with id=AB2, first strand: chain 'E' and resid 329 through 330 removed outlier: 3.929A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 18 through 21 Processing sheet with id=AB4, first strand: chain 'G' and resid 88 through 95 removed outlier: 3.998A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS G 92 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG G 105 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG G 94 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TRP G 103 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 19 through 23 removed outlier: 3.931A pdb=" N ALA H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.916A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR H 86 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP H 92 " --> pdb=" O TYR H 95A" (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR H 95A" --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.697A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.700A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AC3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.267A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY A 451 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N GLN A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.153A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.267A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 303 through 308 Processing sheet with id=AC8, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.810A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AD1, first strand: chain 'C' and resid 18 through 21 Processing sheet with id=AD2, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AD3, first strand: chain 'C' and resid 92 through 95 removed outlier: 4.524A pdb=" N LEU C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AD5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.514A pdb=" N VAL D 47 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 89 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR D 86 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP D 92 " --> pdb=" O TYR D 95A" (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR D 95A" --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.610A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.966A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 120 through 121 Processing sheet with id=AE2, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.492A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N ASN I 448 " --> pdb=" O GLN I 290 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N GLN I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.492A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 303 through 308 Processing sheet with id=AE7, first strand: chain 'I' and resid 329 through 330 removed outlier: 3.664A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 359 through 361 Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 21 Processing sheet with id=AF1, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AF2, first strand: chain 'K' and resid 92 through 95 removed outlier: 4.763A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.938A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 53 through 54 removed outlier: 7.095A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP L 92 " --> pdb=" O TYR L 95A" (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR L 95A" --> pdb=" O ASP L 92 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1563 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: 10.62 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5281 1.03 - 1.23: 15611 1.23 - 1.43: 6339 1.43 - 1.63: 11985 1.63 - 1.83: 162 Bond restraints: 39378 Sorted by residual: bond pdb=" C ARG L 37 " pdb=" O ARG L 37 " ideal model delta sigma weight residual 1.233 1.136 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CD1 TRP C 100C" pdb=" HD1 TRP C 100C" ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CD2 PHE C 67 " pdb=" HD2 PHE C 67 " ideal model delta sigma weight residual 0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CD2 PHE I 353 " pdb=" HD2 PHE I 353 " ideal model delta sigma weight residual 0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" N VAL A 292 " pdb=" H VAL A 292 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 ... (remaining 39373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 65620 4.08 - 8.16: 4514 8.16 - 12.24: 203 12.24 - 16.32: 7 16.32 - 20.40: 2 Bond angle restraints: 70346 Sorted by residual: angle pdb=" N PRO E 253 " pdb=" CA PRO E 253 " pdb=" C PRO E 253 " ideal model delta sigma weight residual 113.65 99.64 14.01 1.35e+00 5.49e-01 1.08e+02 angle pdb=" N PRO A 253 " pdb=" CA PRO A 253 " pdb=" C PRO A 253 " ideal model delta sigma weight residual 114.03 101.46 12.57 1.23e+00 6.61e-01 1.04e+02 angle pdb=" CA ASP C 101 " pdb=" CB ASP C 101 " pdb=" CG ASP C 101 " ideal model delta sigma weight residual 112.60 120.94 -8.34 1.00e+00 1.00e+00 6.96e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" C PRO A 206 " ideal model delta sigma weight residual 114.03 103.99 10.04 1.23e+00 6.61e-01 6.66e+01 angle pdb=" N TYR F 586 " pdb=" CA TYR F 586 " pdb=" C TYR F 586 " ideal model delta sigma weight residual 111.28 102.39 8.89 1.09e+00 8.42e-01 6.65e+01 ... (remaining 70341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 17820 21.67 - 43.33: 1336 43.33 - 65.00: 584 65.00 - 86.67: 249 86.67 - 108.34: 121 Dihedral angle restraints: 20110 sinusoidal: 11986 harmonic: 8124 Sorted by residual: dihedral pdb=" C VAL L 26 " pdb=" N VAL L 26 " pdb=" CA VAL L 26 " pdb=" CB VAL L 26 " ideal model delta harmonic sigma weight residual -122.00 -136.71 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA ASN E 302 " pdb=" C ASN E 302 " pdb=" N THR E 303 " pdb=" CA THR E 303 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 20107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.311: 3411 0.311 - 0.622: 47 0.622 - 0.933: 3 0.933 - 1.244: 0 1.244 - 1.554: 1 Chirality restraints: 3462 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.39e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 ... (remaining 3459 not shown) Planarity restraints: 5735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN I 203 " -0.241 2.00e-02 2.50e+03 3.80e-01 2.17e+03 pdb=" CD GLN I 203 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN I 203 " 0.235 2.00e-02 2.50e+03 pdb=" NE2 GLN I 203 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN I 203 " 0.612 2.00e-02 2.50e+03 pdb="HE22 GLN I 203 " -0.615 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 203 " -0.242 2.00e-02 2.50e+03 3.75e-01 2.10e+03 pdb=" CD GLN E 203 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN E 203 " 0.239 2.00e-02 2.50e+03 pdb=" NE2 GLN E 203 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 203 " 0.601 2.00e-02 2.50e+03 pdb="HE22 GLN E 203 " -0.603 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN I 246 " -0.253 2.00e-02 2.50e+03 3.35e-01 1.68e+03 pdb=" CD GLN I 246 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN I 246 " 0.245 2.00e-02 2.50e+03 pdb=" NE2 GLN I 246 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN I 246 " 0.519 2.00e-02 2.50e+03 pdb="HE22 GLN I 246 " -0.527 2.00e-02 2.50e+03 ... (remaining 5732 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 1137 2.01 - 2.66: 46837 2.66 - 3.31: 116842 3.31 - 3.95: 148719 3.95 - 4.60: 221386 Nonbonded interactions: 534921 Sorted by model distance: nonbonded pdb=" HG3 PRO I 212 " pdb="HG21 VAL I 254 " model vdw 1.366 2.440 nonbonded pdb=" HG SER H 67 " pdb=" OD1 ASP H 69 " model vdw 1.522 2.450 nonbonded pdb=" HG SER L 67 " pdb=" OD1 ASP L 69 " model vdw 1.562 2.450 nonbonded pdb=" HG1 THR I 138 " pdb=" OD1 ASP I 325 " model vdw 1.573 2.450 nonbonded pdb=" HG SER D 67 " pdb=" OD1 ASP D 69 " model vdw 1.588 2.450 ... (remaining 534916 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 32 through 603) selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'f' selection = chain 'q' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'c' selection = chain 'h' selection = chain 'n' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.230 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.990 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.015 0.102 20892 Z= 0.908 Angle : 2.249 20.396 28535 Z= 1.371 Chirality : 0.123 1.554 3462 Planarity : 0.020 0.290 3422 Dihedral : 21.774 108.337 9253 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 2.60 % Allowed : 12.59 % Favored : 84.81 % Rotamer: Outliers : 4.52 % Allowed : 10.14 % Favored : 85.33 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.14), residues: 2343 helix: -2.28 (0.21), residues: 372 sheet: -1.51 (0.29), residues: 279 loop : -2.60 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 429 TYR 0.118 0.020 TYR A 316 PHE 0.080 0.018 PHE A 376 TRP 0.166 0.031 TRP I 427 HIS 0.016 0.004 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01523 (20751) covalent geometry : angle 2.14743 (28151) SS BOND : bond 0.01997 ( 39) SS BOND : angle 2.60946 ( 78) hydrogen bonds : bond 0.18690 ( 600) hydrogen bonds : angle 10.38294 ( 1563) link_ALPHA1-6 : bond 0.01878 ( 6) link_ALPHA1-6 : angle 2.18089 ( 18) link_BETA1-4 : bond 0.02908 ( 60) link_BETA1-4 : angle 7.56654 ( 180) link_NAG-ASN : bond 0.02254 ( 36) link_NAG-ASN : angle 5.74663 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 216 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 215 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7944 (mp) REVERT: F 588 GLU cc_start: 0.8397 (tp30) cc_final: 0.8020 (tp30) REVERT: F 596 TRP cc_start: 0.7897 (m-10) cc_final: 0.7656 (m-10) REVERT: H 48 MET cc_start: 0.2009 (mtp) cc_final: 0.1627 (tmm) REVERT: I 164 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: I 499 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7370 (m) REVERT: J 580 VAL cc_start: 0.9362 (t) cc_final: 0.9147 (p) REVERT: J 588 GLU cc_start: 0.8271 (tp30) cc_final: 0.7998 (tp30) REVERT: J 592 LEU cc_start: 0.9359 (mt) cc_final: 0.8990 (mt) REVERT: J 596 TRP cc_start: 0.7763 (m-10) cc_final: 0.7523 (m-10) outliers start: 95 outliers final: 58 residues processed: 302 average time/residue: 0.3661 time to fit residues: 160.4698 Evaluate side-chains 235 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 478 ASN H 95 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 398 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN I 302 ASN I 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.043329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.037462 restraints weight = 902275.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.038936 restraints weight = 398327.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.039822 restraints weight = 213842.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.040330 restraints weight = 131216.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.040654 restraints weight = 89752.475| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 20892 Z= 0.311 Angle : 1.195 15.018 28535 Z= 0.568 Chirality : 0.060 0.759 3462 Planarity : 0.008 0.155 3422 Dihedral : 18.055 78.658 4783 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.95 % Favored : 87.32 % Rotamer: Outliers : 0.29 % Allowed : 3.48 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.15), residues: 2343 helix: -2.01 (0.22), residues: 378 sheet: -2.13 (0.24), residues: 378 loop : -2.76 (0.13), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 54 TYR 0.022 0.003 TYR E 316 PHE 0.032 0.002 PHE C 91 TRP 0.025 0.003 TRP I 427 HIS 0.010 0.002 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00633 (20751) covalent geometry : angle 1.07383 (28151) SS BOND : bond 0.00534 ( 39) SS BOND : angle 1.48642 ( 78) hydrogen bonds : bond 0.07385 ( 600) hydrogen bonds : angle 8.81689 ( 1563) link_ALPHA1-6 : bond 0.00640 ( 6) link_ALPHA1-6 : angle 1.78398 ( 18) link_BETA1-4 : bond 0.01614 ( 60) link_BETA1-4 : angle 5.14756 ( 180) link_NAG-ASN : bond 0.00836 ( 36) link_NAG-ASN : angle 5.51082 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.8772 (mtp) cc_final: 0.8401 (mtm) REVERT: F 588 GLU cc_start: 0.9593 (tp30) cc_final: 0.9296 (tp30) REVERT: F 596 TRP cc_start: 0.9588 (m-10) cc_final: 0.9351 (m-10) REVERT: G 2 MET cc_start: 0.7976 (mtt) cc_final: 0.7529 (ttp) REVERT: H 48 MET cc_start: 0.3278 (mtp) cc_final: 0.2163 (tmm) REVERT: A 161 MET cc_start: 0.9505 (tpp) cc_final: 0.9122 (tpp) REVERT: A 492 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8848 (pm20) REVERT: B 588 GLU cc_start: 0.9538 (tp30) cc_final: 0.9274 (mm-30) REVERT: I 492 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8974 (pm20) REVERT: J 530 MET cc_start: 0.9108 (mtp) cc_final: 0.8472 (mtm) REVERT: J 584 GLU cc_start: 0.9378 (pt0) cc_final: 0.9142 (pt0) REVERT: L 17 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7325 (mt-10) outliers start: 6 outliers final: 5 residues processed: 193 average time/residue: 0.3982 time to fit residues: 109.0454 Evaluate side-chains 162 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 92 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN L 95 ASN 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 = 0.042669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.036858 restraints weight = 904778.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.038310 restraints weight = 401137.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.039187 restraints weight = 215599.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.039691 restraints weight = 132622.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.040018 restraints weight = 90991.241| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20892 Z= 0.246 Angle : 1.026 15.580 28535 Z= 0.491 Chirality : 0.056 0.588 3462 Planarity : 0.007 0.156 3422 Dihedral : 13.954 59.866 4783 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.15 % Favored : 86.17 % Rotamer: Outliers : 0.14 % Allowed : 3.00 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.15), residues: 2343 helix: -1.77 (0.23), residues: 378 sheet: -2.17 (0.25), residues: 378 loop : -2.75 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 64 TYR 0.023 0.002 TYR H 36 PHE 0.023 0.002 PHE G 67 TRP 0.052 0.003 TRP K 32 HIS 0.009 0.002 HIS K 96 Details of bonding type rmsd covalent geometry : bond 0.00487 (20751) covalent geometry : angle 0.93120 (28151) SS BOND : bond 0.00457 ( 39) SS BOND : angle 1.35701 ( 78) hydrogen bonds : bond 0.06138 ( 600) hydrogen bonds : angle 8.49829 ( 1563) link_ALPHA1-6 : bond 0.00867 ( 6) link_ALPHA1-6 : angle 1.84512 ( 18) link_BETA1-4 : bond 0.01150 ( 60) link_BETA1-4 : angle 4.47938 ( 180) link_NAG-ASN : bond 0.00569 ( 36) link_NAG-ASN : angle 4.09389 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 161 MET cc_start: 0.9217 (tpp) cc_final: 0.9001 (tpp) REVERT: F 588 GLU cc_start: 0.9573 (tp30) cc_final: 0.9257 (tp30) REVERT: G 35 MET cc_start: 0.8724 (tpt) cc_final: 0.8490 (mmm) REVERT: A 492 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8856 (pm20) REVERT: B 584 GLU cc_start: 0.9519 (tt0) cc_final: 0.9144 (tt0) REVERT: B 588 GLU cc_start: 0.9531 (tp30) cc_final: 0.9207 (mm-30) REVERT: D 48 MET cc_start: 0.3525 (mtp) cc_final: 0.2348 (tmm) REVERT: I 161 MET cc_start: 0.9239 (tpt) cc_final: 0.8644 (tpp) REVERT: I 492 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8998 (pm20) REVERT: J 530 MET cc_start: 0.9137 (mtp) cc_final: 0.8550 (mtm) REVERT: J 580 VAL cc_start: 0.9826 (t) cc_final: 0.9556 (p) outliers start: 3 outliers final: 3 residues processed: 180 average time/residue: 0.3833 time to fit residues: 99.7391 Evaluate side-chains 158 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 231 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 ASN ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN K 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.040852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.035240 restraints weight = 924030.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.036669 restraints weight = 416979.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.037523 restraints weight = 226223.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.038017 restraints weight = 141297.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.038349 restraints weight = 98169.823| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20892 Z= 0.299 Angle : 0.986 12.132 28535 Z= 0.481 Chirality : 0.052 0.562 3462 Planarity : 0.007 0.128 3422 Dihedral : 11.202 59.386 4783 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.47 % Favored : 85.02 % Rotamer: Outliers : 0.19 % Allowed : 3.52 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.15), residues: 2343 helix: -1.79 (0.23), residues: 381 sheet: -2.38 (0.25), residues: 393 loop : -2.96 (0.13), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 500 TYR 0.028 0.003 TYR F 638 PHE 0.019 0.002 PHE G 91 TRP 0.020 0.003 TRP A 112 HIS 0.008 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00580 (20751) covalent geometry : angle 0.90822 (28151) SS BOND : bond 0.00489 ( 39) SS BOND : angle 1.30434 ( 78) hydrogen bonds : bond 0.06004 ( 600) hydrogen bonds : angle 8.45508 ( 1563) link_ALPHA1-6 : bond 0.00429 ( 6) link_ALPHA1-6 : angle 1.94343 ( 18) link_BETA1-4 : bond 0.01048 ( 60) link_BETA1-4 : angle 4.10370 ( 180) link_NAG-ASN : bond 0.00598 ( 36) link_NAG-ASN : angle 3.48948 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.8888 (mtp) cc_final: 0.8571 (mtm) REVERT: F 588 GLU cc_start: 0.9553 (tp30) cc_final: 0.9347 (tp30) REVERT: A 100 MET cc_start: 0.9468 (mmm) cc_final: 0.9142 (mmp) REVERT: A 161 MET cc_start: 0.9652 (tpp) cc_final: 0.9382 (tpp) REVERT: A 492 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8957 (mp0) REVERT: B 588 GLU cc_start: 0.9519 (tp30) cc_final: 0.9240 (mm-30) REVERT: I 161 MET cc_start: 0.9292 (tpt) cc_final: 0.8756 (tpp) REVERT: J 530 MET cc_start: 0.9187 (mtp) cc_final: 0.8360 (mtm) REVERT: J 584 GLU cc_start: 0.9436 (pt0) cc_final: 0.9204 (pt0) REVERT: J 588 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9017 (mm-30) outliers start: 4 outliers final: 3 residues processed: 176 average time/residue: 0.3769 time to fit residues: 95.5747 Evaluate side-chains 147 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 82 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.041004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.035383 restraints weight = 922504.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.036802 restraints weight = 416150.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.037669 restraints weight = 226211.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.038161 restraints weight = 140299.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.038493 restraints weight = 97201.042| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20892 Z= 0.257 Angle : 0.927 11.962 28535 Z= 0.454 Chirality : 0.050 0.532 3462 Planarity : 0.006 0.111 3422 Dihedral : 10.615 59.684 4783 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.85 % Favored : 84.64 % Rotamer: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.15), residues: 2343 helix: -1.69 (0.24), residues: 381 sheet: -2.40 (0.25), residues: 390 loop : -2.95 (0.13), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.023 0.002 TYR H 36 PHE 0.021 0.002 PHE K 91 TRP 0.023 0.002 TRP K 103 HIS 0.007 0.002 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00498 (20751) covalent geometry : angle 0.85306 (28151) SS BOND : bond 0.00655 ( 39) SS BOND : angle 1.60965 ( 78) hydrogen bonds : bond 0.05559 ( 600) hydrogen bonds : angle 8.30963 ( 1563) link_ALPHA1-6 : bond 0.00458 ( 6) link_ALPHA1-6 : angle 1.68237 ( 18) link_BETA1-4 : bond 0.00977 ( 60) link_BETA1-4 : angle 3.83510 ( 180) link_NAG-ASN : bond 0.00562 ( 36) link_NAG-ASN : angle 3.20370 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.8891 (mtp) cc_final: 0.8340 (mtm) REVERT: A 492 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8934 (mp0) REVERT: B 530 MET cc_start: 0.8226 (mtt) cc_final: 0.7733 (mtt) REVERT: B 588 GLU cc_start: 0.9506 (tp30) cc_final: 0.9266 (mm-30) REVERT: B 626 MET cc_start: 0.9208 (mmp) cc_final: 0.8863 (mmm) REVERT: C 2 MET cc_start: 0.8157 (mtt) cc_final: 0.7796 (mtm) REVERT: I 161 MET cc_start: 0.9266 (tpt) cc_final: 0.8710 (tpp) REVERT: J 530 MET cc_start: 0.9177 (mtp) cc_final: 0.8252 (mtm) REVERT: J 584 GLU cc_start: 0.9425 (pt0) cc_final: 0.9192 (pt0) REVERT: J 588 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9011 (mm-30) outliers start: 5 outliers final: 5 residues processed: 172 average time/residue: 0.3591 time to fit residues: 90.3159 Evaluate side-chains 149 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 171 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** 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 = 0.3145 r_free = 0.3145 target = 0.034568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.026519 restraints weight = 665088.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.028266 restraints weight = 320465.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.029469 restraints weight = 187204.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.030339 restraints weight = 123809.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.030944 restraints weight = 88892.508| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 20892 Z= 0.165 Angle : 0.851 14.555 28535 Z= 0.412 Chirality : 0.049 0.458 3462 Planarity : 0.005 0.083 3422 Dihedral : 9.984 58.466 4783 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.53 % Favored : 86.00 % Rotamer: Outliers : 0.10 % Allowed : 1.48 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.15), residues: 2343 helix: -1.75 (0.23), residues: 402 sheet: -2.59 (0.24), residues: 387 loop : -2.82 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 500 TYR 0.050 0.002 TYR K 56 PHE 0.016 0.002 PHE H 62 TRP 0.017 0.002 TRP E 112 HIS 0.006 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00343 (20751) covalent geometry : angle 0.77936 (28151) SS BOND : bond 0.00750 ( 39) SS BOND : angle 2.06266 ( 78) hydrogen bonds : bond 0.04764 ( 600) hydrogen bonds : angle 7.91659 ( 1563) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 1.54686 ( 18) link_BETA1-4 : bond 0.01060 ( 60) link_BETA1-4 : angle 3.58101 ( 180) link_NAG-ASN : bond 0.00372 ( 36) link_NAG-ASN : angle 2.87239 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.8975 (mtp) cc_final: 0.8502 (mtm) REVERT: F 588 GLU cc_start: 0.9626 (tp30) cc_final: 0.9341 (tp30) REVERT: A 492 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8867 (pm20) REVERT: B 530 MET cc_start: 0.8276 (mtt) cc_final: 0.7709 (mtt) REVERT: B 588 GLU cc_start: 0.9519 (tp30) cc_final: 0.9237 (mm-30) REVERT: B 626 MET cc_start: 0.9206 (mmp) cc_final: 0.8959 (mmm) REVERT: C 35 MET cc_start: 0.8945 (tpt) cc_final: 0.8177 (tpp) REVERT: I 161 MET cc_start: 0.9291 (tpt) cc_final: 0.8844 (tpp) REVERT: J 580 VAL cc_start: 0.9814 (t) cc_final: 0.9578 (p) REVERT: J 584 GLU cc_start: 0.9441 (pt0) cc_final: 0.9133 (pt0) REVERT: J 588 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9056 (mm-30) REVERT: K 2 MET cc_start: 0.8241 (mtt) cc_final: 0.8003 (mtm) outliers start: 2 outliers final: 2 residues processed: 167 average time/residue: 0.3705 time to fit residues: 90.2463 Evaluate side-chains 142 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 189 optimal weight: 0.0980 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 ASN ** I 103 GLN ** 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 = 0.3129 r_free = 0.3129 target = 0.034106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.026158 restraints weight = 668895.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.027863 restraints weight = 322502.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.029041 restraints weight = 188995.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.029905 restraints weight = 125725.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.030497 restraints weight = 90304.281| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20892 Z= 0.205 Angle : 0.843 11.610 28535 Z= 0.411 Chirality : 0.048 0.491 3462 Planarity : 0.006 0.178 3422 Dihedral : 9.722 57.327 4783 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.43 % Favored : 85.06 % Rotamer: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.16), residues: 2343 helix: -1.46 (0.24), residues: 384 sheet: -2.34 (0.25), residues: 399 loop : -2.77 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.028 0.002 TYR K 56 PHE 0.022 0.002 PHE A 391 TRP 0.025 0.002 TRP C 32 HIS 0.005 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00412 (20751) covalent geometry : angle 0.77549 (28151) SS BOND : bond 0.00497 ( 39) SS BOND : angle 1.80526 ( 78) hydrogen bonds : bond 0.04868 ( 600) hydrogen bonds : angle 7.86163 ( 1563) link_ALPHA1-6 : bond 0.00569 ( 6) link_ALPHA1-6 : angle 1.64472 ( 18) link_BETA1-4 : bond 0.01015 ( 60) link_BETA1-4 : angle 3.48411 ( 180) link_NAG-ASN : bond 0.00466 ( 36) link_NAG-ASN : angle 2.81840 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.8981 (mtp) cc_final: 0.8475 (mtm) REVERT: A 492 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8866 (pm20) REVERT: B 530 MET cc_start: 0.8395 (mtt) cc_final: 0.7882 (mtt) REVERT: B 588 GLU cc_start: 0.9518 (tp30) cc_final: 0.9237 (mm-30) REVERT: B 626 MET cc_start: 0.9227 (mmp) cc_final: 0.9003 (mmm) REVERT: C 35 MET cc_start: 0.8973 (tpt) cc_final: 0.8707 (tpp) REVERT: J 530 MET cc_start: 0.9230 (mtp) cc_final: 0.8508 (mtm) REVERT: J 584 GLU cc_start: 0.9437 (pt0) cc_final: 0.9197 (pt0) REVERT: J 588 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9035 (mm-30) REVERT: L 17 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6965 (mt-10) outliers start: 2 outliers final: 2 residues processed: 165 average time/residue: 0.3686 time to fit residues: 88.0600 Evaluate side-chains 143 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 15 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.041330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.035653 restraints weight = 914188.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.037090 restraints weight = 407240.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.037954 restraints weight = 221294.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.038445 restraints weight = 137544.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.038771 restraints weight = 95564.149| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20892 Z= 0.203 Angle : 0.826 11.534 28535 Z= 0.405 Chirality : 0.048 0.493 3462 Planarity : 0.005 0.070 3422 Dihedral : 9.478 56.925 4783 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.60 % Favored : 84.89 % Rotamer: Outliers : 0.10 % Allowed : 1.24 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.15), residues: 2343 helix: -1.42 (0.24), residues: 384 sheet: -2.46 (0.24), residues: 399 loop : -2.76 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.034 0.002 TYR K 56 PHE 0.012 0.002 PHE K 91 TRP 0.016 0.002 TRP A 479 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00398 (20751) covalent geometry : angle 0.76254 (28151) SS BOND : bond 0.00403 ( 39) SS BOND : angle 1.61291 ( 78) hydrogen bonds : bond 0.04798 ( 600) hydrogen bonds : angle 7.80513 ( 1563) link_ALPHA1-6 : bond 0.00673 ( 6) link_ALPHA1-6 : angle 1.68598 ( 18) link_BETA1-4 : bond 0.00994 ( 60) link_BETA1-4 : angle 3.37396 ( 180) link_NAG-ASN : bond 0.00392 ( 36) link_NAG-ASN : angle 2.70949 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.8859 (mtp) cc_final: 0.8078 (mtm) REVERT: F 588 GLU cc_start: 0.9602 (tp30) cc_final: 0.9354 (tp30) REVERT: A 492 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8919 (pm20) REVERT: B 588 GLU cc_start: 0.9493 (tp30) cc_final: 0.9207 (mm-30) REVERT: J 580 VAL cc_start: 0.9840 (t) cc_final: 0.9598 (p) REVERT: J 584 GLU cc_start: 0.9408 (pt0) cc_final: 0.9152 (pt0) REVERT: J 588 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9006 (mm-30) outliers start: 2 outliers final: 2 residues processed: 164 average time/residue: 0.3671 time to fit residues: 87.2056 Evaluate side-chains 142 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 146 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.032657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.025111 restraints weight = 716568.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.026664 restraints weight = 353688.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.027726 restraints weight = 210657.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.028528 restraints weight = 142933.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.029085 restraints weight = 104268.885| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 20892 Z= 0.339 Angle : 0.939 11.890 28535 Z= 0.470 Chirality : 0.049 0.501 3462 Planarity : 0.006 0.091 3422 Dihedral : 9.780 59.985 4783 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.24 % Favored : 82.24 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.15), residues: 2343 helix: -1.66 (0.24), residues: 378 sheet: -2.85 (0.25), residues: 357 loop : -3.01 (0.13), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 298 TYR 0.039 0.003 TYR I 217 PHE 0.020 0.003 PHE I 176 TRP 0.020 0.003 TRP A 479 HIS 0.011 0.002 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00654 (20751) covalent geometry : angle 0.88227 (28151) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.58426 ( 78) hydrogen bonds : bond 0.05771 ( 600) hydrogen bonds : angle 8.33693 ( 1563) link_ALPHA1-6 : bond 0.00381 ( 6) link_ALPHA1-6 : angle 1.89048 ( 18) link_BETA1-4 : bond 0.00983 ( 60) link_BETA1-4 : angle 3.39842 ( 180) link_NAG-ASN : bond 0.00812 ( 36) link_NAG-ASN : angle 2.85914 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.9059 (mtp) cc_final: 0.8588 (mtm) REVERT: F 584 GLU cc_start: 0.9560 (tt0) cc_final: 0.8938 (mt-10) REVERT: F 588 GLU cc_start: 0.9643 (tp30) cc_final: 0.9427 (tp30) REVERT: B 530 MET cc_start: 0.8447 (mtt) cc_final: 0.7735 (mtt) REVERT: C 35 MET cc_start: 0.8598 (tpp) cc_final: 0.7924 (tpp) REVERT: J 588 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8992 (mm-30) REVERT: L 48 MET cc_start: 0.7873 (ttp) cc_final: 0.6849 (tmm) outliers start: 2 outliers final: 2 residues processed: 157 average time/residue: 0.3755 time to fit residues: 85.3724 Evaluate side-chains 131 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 46 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.033890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026030 restraints weight = 681544.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.027691 restraints weight = 332614.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.028878 restraints weight = 196228.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.029722 restraints weight = 130169.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.030275 restraints weight = 94251.130| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20892 Z= 0.162 Angle : 0.803 11.194 28535 Z= 0.393 Chirality : 0.048 0.467 3462 Planarity : 0.005 0.076 3422 Dihedral : 9.330 59.988 4783 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.34 % Favored : 85.15 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.15), residues: 2343 helix: -1.43 (0.24), residues: 378 sheet: -2.63 (0.24), residues: 390 loop : -2.78 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 38 TYR 0.034 0.002 TYR K 56 PHE 0.015 0.002 PHE H 62 TRP 0.020 0.002 TRP G 32 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00333 (20751) covalent geometry : angle 0.74401 (28151) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.68133 ( 78) hydrogen bonds : bond 0.04527 ( 600) hydrogen bonds : angle 7.83416 ( 1563) link_ALPHA1-6 : bond 0.00617 ( 6) link_ALPHA1-6 : angle 1.53242 ( 18) link_BETA1-4 : bond 0.01049 ( 60) link_BETA1-4 : angle 3.19829 ( 180) link_NAG-ASN : bond 0.00339 ( 36) link_NAG-ASN : angle 2.58409 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 MET cc_start: 0.9048 (mtp) cc_final: 0.8612 (mtm) REVERT: A 100 MET cc_start: 0.9650 (mmp) cc_final: 0.9436 (mmp) REVERT: A 492 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8878 (mp0) REVERT: B 530 MET cc_start: 0.8453 (mtt) cc_final: 0.7734 (mtt) REVERT: B 584 GLU cc_start: 0.9482 (tt0) cc_final: 0.8820 (mt-10) REVERT: B 588 GLU cc_start: 0.9485 (tp30) cc_final: 0.9255 (mm-30) REVERT: C 35 MET cc_start: 0.8580 (tpp) cc_final: 0.7613 (tpp) REVERT: C 103 TRP cc_start: 0.8429 (t-100) cc_final: 0.8151 (t-100) REVERT: J 530 MET cc_start: 0.9193 (mtp) cc_final: 0.8536 (mtm) REVERT: J 580 VAL cc_start: 0.9809 (t) cc_final: 0.9603 (p) REVERT: J 584 GLU cc_start: 0.9452 (pt0) cc_final: 0.9226 (pt0) REVERT: J 588 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9059 (mm-30) REVERT: K 35 MET cc_start: 0.8882 (tpt) cc_final: 0.8298 (tpp) outliers start: 2 outliers final: 2 residues processed: 155 average time/residue: 0.3780 time to fit residues: 84.5292 Evaluate side-chains 135 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 179 optimal weight: 0.0770 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** 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 = 0.3385 r_free = 0.3385 target = 0.040659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.034985 restraints weight = 923882.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.036414 restraints weight = 409272.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.037266 restraints weight = 221879.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.037768 restraints weight = 139109.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.038082 restraints weight = 96914.629| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20892 Z= 0.201 Angle : 0.797 11.298 28535 Z= 0.392 Chirality : 0.046 0.454 3462 Planarity : 0.005 0.070 3422 Dihedral : 9.054 57.148 4783 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 15.11 % Favored : 84.38 % Rotamer: Outliers : 0.10 % Allowed : 0.81 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.16), residues: 2343 helix: -1.40 (0.25), residues: 378 sheet: -2.66 (0.25), residues: 366 loop : -2.73 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 298 TYR 0.020 0.002 TYR D 32 PHE 0.013 0.002 PHE E 391 TRP 0.039 0.002 TRP A 479 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00394 (20751) covalent geometry : angle 0.73874 (28151) SS BOND : bond 0.00378 ( 39) SS BOND : angle 1.46277 ( 78) hydrogen bonds : bond 0.04628 ( 600) hydrogen bonds : angle 7.79098 ( 1563) link_ALPHA1-6 : bond 0.00507 ( 6) link_ALPHA1-6 : angle 1.66276 ( 18) link_BETA1-4 : bond 0.01016 ( 60) link_BETA1-4 : angle 3.17820 ( 180) link_NAG-ASN : bond 0.00438 ( 36) link_NAG-ASN : angle 2.59493 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4781.20 seconds wall clock time: 83 minutes 14.16 seconds (4994.16 seconds total)