Starting phenix.real_space_refine on Thu Feb 5 16:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dim_46914/02_2026/9dim_46914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dim_46914/02_2026/9dim_46914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dim_46914/02_2026/9dim_46914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dim_46914/02_2026/9dim_46914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dim_46914/02_2026/9dim_46914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dim_46914/02_2026/9dim_46914.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 11517 2.51 5 N 3014 2.21 5 O 3739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18385 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3477 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 937 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "C" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3477 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 938 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "G" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3477 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 938 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "M" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1015 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "N" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 836 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "E" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1015 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 836 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.85, per 1000 atoms: 0.21 Number of scatterers: 18385 At special positions: 0 Unit cell: (125.426, 147.56, 155.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3739 8.00 N 3014 7.00 C 11517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.05 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.08 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.12 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.05 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 332 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.12 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.05 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.11 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 332 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.11 Simple disulfide: pdb=" SG CYS N 27C" - pdb=" SG CYS N 28 " distance=2.30 Simple disulfide: pdb=" SG CYS N 89 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 27C" - pdb=" SG CYS F 28 " distance=2.27 Simple disulfide: pdb=" SG CYS F 89 " - pdb=" SG CYS F 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN H 4 " - " MAN H 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " " MAN H 6 " - " MAN H 8 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " " BMA Z 3 " - " MAN Z 5 " " BMA c 3 " - " MAN c 5 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG R 1 " - " FUC R 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG b 1 " - " FUC b 4 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 448 " " NAG A 603 " - " ASN A 340 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 448 " " NAG C 603 " - " ASN C 465 " " NAG C 604 " - " ASN C 340 " " NAG C 605 " - " ASN C 133 " " NAG C 606 " - " ASN C 160 " " NAG C 607 " - " ASN C 241 " " NAG D 701 " - " ASN D 611 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 448 " " NAG G 603 " - " ASN G 340 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 241 " " NAG H 1 " - " ASN A 88 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 625 " " NAG J 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 301 " " NAG L 1 " - " ASN A 333 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN A 465 " " NAG R 1 " - " ASN B 625 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 301 " " NAG V 1 " - " ASN C 333 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN D 625 " " NAG c 1 " - " ASN G 88 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN G 333 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 465 " " NAG i 1 " - " ASN G 156 " " NAG j 1 " - " ASN G 197 " " NAG k 1 " - " ASN G 234 " " NAG l 1 " - " ASN G 262 " " NAG m 1 " - " ASN G 276 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 908.7 milliseconds 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3990 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 29 sheets defined 21.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.625A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.677A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.548A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.735A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 596 removed outlier: 3.824A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.646A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 336 through 351 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.225A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.104A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 596 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 336 through 351 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 484 removed outlier: 4.093A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.913A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG I 542 " --> pdb=" O THR I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 596 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 664 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.616A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.622A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.216A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.808A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.362A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 307 removed outlier: 4.064A pdb=" N ASN A 301 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 317 through 324 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.254A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.779A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.361A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 283 through 312 removed outlier: 6.490A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 324 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.246A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.980A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.290A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 283 through 307 removed outlier: 3.608A pdb=" N ASN G 301 " --> pdb=" O ILE G 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 317 through 324 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AC4, first strand: chain 'M' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 18 through 27 current: chain 'M' and resid 73 through 82 Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 12 current: chain 'M' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 102 through 103 Processing sheet with id=AC6, first strand: chain 'N' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 14 current: chain 'N' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 53 through 54 current: chain 'N' and resid 97 through 98 Processing sheet with id=AC7, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AC8, first strand: chain 'E' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 27 current: chain 'E' and resid 74 through 82 Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 58 current: chain 'E' and resid 100F through 103 Processing sheet with id=AD1, first strand: chain 'F' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 9 through 14 current: chain 'F' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 53 through 54 current: chain 'F' and resid 97 through 98 Processing sheet with id=AD2, first strand: chain 'F' and resid 19 through 24 461 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3653 1.32 - 1.46: 5580 1.46 - 1.59: 9378 1.59 - 1.72: 0 1.72 - 1.85: 148 Bond restraints: 18759 Sorted by residual: bond pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 1.472 1.436 0.036 1.21e-02 6.83e+03 8.90e+00 bond pdb=" CG ASP F 51 " pdb=" OD1 ASP F 51 " ideal model delta sigma weight residual 1.249 1.194 0.055 1.90e-02 2.77e+03 8.37e+00 bond pdb=" CG ASP B 632 " pdb=" OD2 ASP B 632 " ideal model delta sigma weight residual 1.249 1.196 0.053 1.90e-02 2.77e+03 7.65e+00 bond pdb=" CG ASP G 477 " pdb=" OD2 ASP G 477 " ideal model delta sigma weight residual 1.249 1.197 0.052 1.90e-02 2.77e+03 7.46e+00 bond pdb=" CG ASP D 632 " pdb=" OD2 ASP D 632 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.24e+00 ... (remaining 18754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23687 2.39 - 4.78: 1556 4.78 - 7.17: 228 7.17 - 9.56: 12 9.56 - 11.95: 1 Bond angle restraints: 25484 Sorted by residual: angle pdb=" C ALA F 43 " pdb=" N PRO F 44 " pdb=" CA PRO F 44 " ideal model delta sigma weight residual 120.03 127.70 -7.67 9.90e-01 1.02e+00 6.00e+01 angle pdb=" C THR G 219 " pdb=" N PRO G 220 " pdb=" CA PRO G 220 " ideal model delta sigma weight residual 119.78 127.39 -7.61 1.03e+00 9.43e-01 5.46e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.04 -7.48 1.02e+00 9.61e-01 5.38e+01 angle pdb=" C ALA N 43 " pdb=" N PRO N 44 " pdb=" CA PRO N 44 " ideal model delta sigma weight residual 120.03 127.29 -7.26 9.90e-01 1.02e+00 5.38e+01 angle pdb=" C ARG G 469 " pdb=" N PRO G 470 " pdb=" CA PRO G 470 " ideal model delta sigma weight residual 120.03 127.09 -7.06 9.90e-01 1.02e+00 5.09e+01 ... (remaining 25479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 12133 22.25 - 44.50: 278 44.50 - 66.75: 73 66.75 - 89.00: 109 89.00 - 111.25: 64 Dihedral angle restraints: 12657 sinusoidal: 6465 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS N 89 " pdb=" SG CYS N 89 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 170.89 -77.89 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS F 89 " pdb=" SG CYS F 89 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 169.19 -76.19 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.18 45.18 1 1.00e+01 1.00e-02 2.83e+01 ... (remaining 12654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 3137 0.209 - 0.418: 33 0.418 - 0.626: 5 0.626 - 0.835: 2 0.835 - 1.044: 3 Chirality restraints: 3180 Sorted by residual: chirality pdb=" C1 MAN H 6 " pdb=" O6 BMA H 3 " pdb=" C2 MAN H 6 " pdb=" O5 MAN H 6 " both_signs ideal model delta sigma weight residual False 2.40 1.36 1.04 2.00e-02 2.50e+03 2.72e+03 chirality pdb=" C1 MAN H 8 " pdb=" O6 MAN H 6 " pdb=" C2 MAN H 8 " pdb=" O5 MAN H 8 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.75e+03 chirality pdb=" C1 MAN S 4 " pdb=" O6 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 1.73 0.67 2.00e-02 2.50e+03 1.12e+03 ... (remaining 3177 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.080 2.00e-02 2.50e+03 8.42e-02 8.86e+01 pdb=" CG ASN C 392 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.134 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " 0.068 2.00e-02 2.50e+03 7.08e-02 6.27e+01 pdb=" CG ASN A 392 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " -0.111 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 333 " -0.068 2.00e-02 2.50e+03 7.05e-02 6.22e+01 pdb=" CG ASN C 333 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 333 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 333 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.084 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 93 2.60 - 3.17: 15586 3.17 - 3.75: 26750 3.75 - 4.32: 40259 4.32 - 4.90: 63871 Nonbonded interactions: 146559 Sorted by model distance: nonbonded pdb=" O3 NAG R 2 " pdb=" O7 NAG R 2 " model vdw 2.019 3.040 nonbonded pdb=" O3 NAG a 1 " pdb=" O7 NAG a 1 " model vdw 2.142 3.040 nonbonded pdb=" C3 NAG R 2 " pdb=" O7 NAG R 2 " model vdw 2.216 3.470 nonbonded pdb=" C3 NAG a 1 " pdb=" O7 NAG a 1 " model vdw 2.222 3.470 nonbonded pdb=" O3 NAG a 1 " pdb=" O5 NAG a 2 " model vdw 2.358 3.040 ... (remaining 146554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 32 through 603) selection = (chain 'G' and resid 32 through 603) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 520 through 663 or (resid 664 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2)) or resid 701)) selection = (chain 'I' and (resid 520 through 663 or (resid 664 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2)) or resid 701)) } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = (chain 'H' and (resid 2 or resid 5 through 8)) selection = (chain 'S' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'm' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) } ncs_group { reference = chain 'Z' selection = chain 'c' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.410 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.013 0.267 18910 Z= 0.679 Angle : 1.364 13.574 25896 Z= 0.832 Chirality : 0.081 1.044 3180 Planarity : 0.005 0.044 3080 Dihedral : 15.706 111.253 8544 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.33 (0.18), residues: 2101 helix: -0.27 (0.22), residues: 438 sheet: 1.71 (0.20), residues: 599 loop : 2.60 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 54 TYR 0.031 0.003 TYR G 217 PHE 0.020 0.004 PHE A 383 TRP 0.027 0.006 TRP C 96 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.01207 (18759) covalent geometry : angle 1.30219 (25484) SS BOND : bond 0.06512 ( 41) SS BOND : angle 4.09671 ( 82) hydrogen bonds : bond 0.18813 ( 461) hydrogen bonds : angle 6.73025 ( 1236) link_ALPHA1-2 : bond 0.00263 ( 1) link_ALPHA1-2 : angle 0.94136 ( 3) link_ALPHA1-3 : bond 0.00521 ( 7) link_ALPHA1-3 : angle 1.39176 ( 21) link_ALPHA1-6 : bond 0.00827 ( 7) link_ALPHA1-6 : angle 5.07403 ( 21) link_BETA1-4 : bond 0.00398 ( 45) link_BETA1-4 : angle 2.29049 ( 135) link_BETA1-6 : bond 0.00812 ( 2) link_BETA1-6 : angle 3.60160 ( 6) link_NAG-ASN : bond 0.06530 ( 48) link_NAG-ASN : angle 3.91096 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9032 (mtp) cc_final: 0.8732 (mtm) REVERT: A 428 GLN cc_start: 0.7831 (mp10) cc_final: 0.7422 (mp10) REVERT: C 68 VAL cc_start: 0.8913 (p) cc_final: 0.8690 (p) REVERT: C 169 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7566 (mtm-85) REVERT: C 228 CYS cc_start: 0.6736 (t) cc_final: 0.6449 (t) REVERT: C 341 LYS cc_start: 0.7678 (mttt) cc_final: 0.7366 (mmtm) REVERT: I 653 GLN cc_start: 0.7802 (tt0) cc_final: 0.7532 (tt0) REVERT: F 87 TYR cc_start: 0.8378 (m-80) cc_final: 0.8157 (m-80) REVERT: F 97 VAL cc_start: 0.8096 (t) cc_final: 0.7848 (m) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1551 time to fit residues: 83.7027 Evaluate side-chains 205 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 280 ASN A 462 ASN C 428 GLN G 82 GLN G 195 ASN I 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135554 restraints weight = 23546.057| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.11 r_work: 0.3484 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18910 Z= 0.153 Angle : 0.699 9.803 25896 Z= 0.325 Chirality : 0.046 0.320 3180 Planarity : 0.004 0.039 3080 Dihedral : 11.962 99.427 4542 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.58 % Allowed : 5.12 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.39 (0.18), residues: 2101 helix: 1.57 (0.26), residues: 396 sheet: 1.37 (0.19), residues: 620 loop : 2.00 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 42 TYR 0.022 0.001 TYR C 191 PHE 0.017 0.002 PHE G 176 TRP 0.023 0.001 TRP N 38 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00334 (18759) covalent geometry : angle 0.64699 (25484) SS BOND : bond 0.00413 ( 41) SS BOND : angle 1.21612 ( 82) hydrogen bonds : bond 0.05520 ( 461) hydrogen bonds : angle 5.08788 ( 1236) link_ALPHA1-2 : bond 0.00671 ( 1) link_ALPHA1-2 : angle 1.20972 ( 3) link_ALPHA1-3 : bond 0.01564 ( 7) link_ALPHA1-3 : angle 2.32249 ( 21) link_ALPHA1-6 : bond 0.02702 ( 7) link_ALPHA1-6 : angle 2.53286 ( 21) link_BETA1-4 : bond 0.00601 ( 45) link_BETA1-4 : angle 2.04852 ( 135) link_BETA1-6 : bond 0.00524 ( 2) link_BETA1-6 : angle 1.54014 ( 6) link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 2.65644 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLN cc_start: 0.8103 (mp10) cc_final: 0.7450 (mp10) REVERT: C 169 ARG cc_start: 0.7844 (mmt-90) cc_final: 0.7385 (mtm-85) REVERT: C 341 LYS cc_start: 0.7628 (mttt) cc_final: 0.7339 (mmtm) REVERT: G 33 ASN cc_start: 0.7910 (m-40) cc_final: 0.7609 (t0) REVERT: N 54 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.7071 (mtm-85) REVERT: F 74 THR cc_start: 0.8185 (m) cc_final: 0.7582 (p) REVERT: F 97 VAL cc_start: 0.8148 (t) cc_final: 0.7745 (m) outliers start: 30 outliers final: 20 residues processed: 233 average time/residue: 0.1371 time to fit residues: 48.0898 Evaluate side-chains 196 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 636 ASN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126789 restraints weight = 23760.203| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.10 r_work: 0.3349 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18910 Z= 0.221 Angle : 0.693 9.080 25896 Z= 0.328 Chirality : 0.048 0.263 3180 Planarity : 0.004 0.038 3080 Dihedral : 8.736 74.081 4542 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.85 % Allowed : 6.23 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.18), residues: 2101 helix: 1.48 (0.27), residues: 396 sheet: 1.23 (0.21), residues: 580 loop : 1.35 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 503 TYR 0.015 0.002 TYR G 217 PHE 0.019 0.002 PHE G 383 TRP 0.020 0.002 TRP M 50 HIS 0.006 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00532 (18759) covalent geometry : angle 0.64310 (25484) SS BOND : bond 0.00538 ( 41) SS BOND : angle 1.51780 ( 82) hydrogen bonds : bond 0.05515 ( 461) hydrogen bonds : angle 4.94232 ( 1236) link_ALPHA1-2 : bond 0.00454 ( 1) link_ALPHA1-2 : angle 1.35993 ( 3) link_ALPHA1-3 : bond 0.01399 ( 7) link_ALPHA1-3 : angle 1.96877 ( 21) link_ALPHA1-6 : bond 0.02374 ( 7) link_ALPHA1-6 : angle 3.12583 ( 21) link_BETA1-4 : bond 0.00512 ( 45) link_BETA1-4 : angle 1.89465 ( 135) link_BETA1-6 : bond 0.00150 ( 2) link_BETA1-6 : angle 1.42891 ( 6) link_NAG-ASN : bond 0.00445 ( 48) link_NAG-ASN : angle 2.51574 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8638 (ptm-80) cc_final: 0.8412 (ptm-80) REVERT: A 114 GLN cc_start: 0.8583 (tt0) cc_final: 0.8380 (tt0) REVERT: A 428 GLN cc_start: 0.8375 (mp10) cc_final: 0.7568 (mp10) REVERT: C 169 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7525 (mtm-85) REVERT: C 341 LYS cc_start: 0.7764 (mttt) cc_final: 0.7530 (mmtm) REVERT: F 77 ASP cc_start: 0.7673 (t0) cc_final: 0.7447 (t0) REVERT: F 97 VAL cc_start: 0.8316 (t) cc_final: 0.7933 (m) outliers start: 35 outliers final: 29 residues processed: 208 average time/residue: 0.1245 time to fit residues: 39.2751 Evaluate side-chains 196 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 146 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 37 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132221 restraints weight = 23654.877| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.01 r_work: 0.3411 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18910 Z= 0.111 Angle : 0.575 9.597 25896 Z= 0.269 Chirality : 0.043 0.272 3180 Planarity : 0.003 0.036 3080 Dihedral : 7.318 66.191 4542 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.58 % Allowed : 6.97 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2101 helix: 1.90 (0.27), residues: 396 sheet: 1.29 (0.21), residues: 587 loop : 1.22 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 42 TYR 0.016 0.001 TYR C 191 PHE 0.011 0.001 PHE C 176 TRP 0.014 0.001 TRP M 50 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00235 (18759) covalent geometry : angle 0.53018 (25484) SS BOND : bond 0.00426 ( 41) SS BOND : angle 1.32992 ( 82) hydrogen bonds : bond 0.04229 ( 461) hydrogen bonds : angle 4.51361 ( 1236) link_ALPHA1-2 : bond 0.00324 ( 1) link_ALPHA1-2 : angle 1.47823 ( 3) link_ALPHA1-3 : bond 0.01427 ( 7) link_ALPHA1-3 : angle 2.09815 ( 21) link_ALPHA1-6 : bond 0.02108 ( 7) link_ALPHA1-6 : angle 2.81857 ( 21) link_BETA1-4 : bond 0.00479 ( 45) link_BETA1-4 : angle 1.65603 ( 135) link_BETA1-6 : bond 0.00296 ( 2) link_BETA1-6 : angle 1.39205 ( 6) link_NAG-ASN : bond 0.00206 ( 48) link_NAG-ASN : angle 2.03837 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 428 GLN cc_start: 0.8346 (mp10) cc_final: 0.7581 (mp10) REVERT: C 169 ARG cc_start: 0.8156 (mmt-90) cc_final: 0.7479 (mtm-85) REVERT: N 54 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7285 (mtm-85) REVERT: E 79 TYR cc_start: 0.7416 (m-80) cc_final: 0.7176 (m-80) REVERT: E 80 MET cc_start: 0.7525 (ttp) cc_final: 0.7065 (ttp) REVERT: F 77 ASP cc_start: 0.7573 (t0) cc_final: 0.7311 (t0) REVERT: F 97 VAL cc_start: 0.8378 (t) cc_final: 0.7968 (m) outliers start: 30 outliers final: 20 residues processed: 203 average time/residue: 0.1365 time to fit residues: 41.8984 Evaluate side-chains 188 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 89 CYS Chi-restraints excluded: chain E residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN G 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.157667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122864 restraints weight = 24886.093| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.04 r_work: 0.3333 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 18910 Z= 0.285 Angle : 0.723 9.657 25896 Z= 0.345 Chirality : 0.049 0.253 3180 Planarity : 0.005 0.041 3080 Dihedral : 7.543 58.881 4542 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.95 % Allowed : 7.45 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2101 helix: 1.38 (0.27), residues: 378 sheet: 0.97 (0.21), residues: 591 loop : 0.80 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 503 TYR 0.019 0.002 TYR G 484 PHE 0.021 0.003 PHE G 159 TRP 0.020 0.002 TRP M 50 HIS 0.007 0.002 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00703 (18759) covalent geometry : angle 0.67903 (25484) SS BOND : bond 0.00518 ( 41) SS BOND : angle 1.86651 ( 82) hydrogen bonds : bond 0.05578 ( 461) hydrogen bonds : angle 4.98843 ( 1236) link_ALPHA1-2 : bond 0.00543 ( 1) link_ALPHA1-2 : angle 1.30949 ( 3) link_ALPHA1-3 : bond 0.01278 ( 7) link_ALPHA1-3 : angle 1.80600 ( 21) link_ALPHA1-6 : bond 0.02092 ( 7) link_ALPHA1-6 : angle 2.87826 ( 21) link_BETA1-4 : bond 0.00429 ( 45) link_BETA1-4 : angle 1.73725 ( 135) link_BETA1-6 : bond 0.00113 ( 2) link_BETA1-6 : angle 1.51800 ( 6) link_NAG-ASN : bond 0.00573 ( 48) link_NAG-ASN : angle 2.40787 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.681 Fit side-chains REVERT: A 46 ARG cc_start: 0.8374 (ptm-80) cc_final: 0.8068 (ptm-80) REVERT: A 428 GLN cc_start: 0.8450 (mp10) cc_final: 0.7468 (mp10) REVERT: C 169 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.7374 (mtm-85) REVERT: G 328 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7442 (mtm-85) REVERT: G 343 LEU cc_start: 0.7891 (mt) cc_final: 0.7688 (mp) REVERT: G 500 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7750 (mmm-85) REVERT: N 12 SER cc_start: 0.7906 (p) cc_final: 0.7612 (t) REVERT: E 80 MET cc_start: 0.7477 (ttp) cc_final: 0.7087 (ttp) REVERT: F 77 ASP cc_start: 0.7538 (t0) cc_final: 0.7148 (t0) outliers start: 37 outliers final: 31 residues processed: 215 average time/residue: 0.1427 time to fit residues: 45.5578 Evaluate side-chains 200 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 155 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 188 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 425 ASN I 575 GLN F 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127171 restraints weight = 23630.907| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.03 r_work: 0.3361 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18910 Z= 0.130 Angle : 0.585 9.466 25896 Z= 0.277 Chirality : 0.044 0.219 3180 Planarity : 0.004 0.048 3080 Dihedral : 7.046 57.999 4542 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.69 % Allowed : 8.72 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.18), residues: 2101 helix: 1.63 (0.27), residues: 396 sheet: 1.16 (0.21), residues: 570 loop : 0.70 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 42 TYR 0.014 0.001 TYR C 191 PHE 0.012 0.001 PHE G 53 TRP 0.015 0.001 TRP M 50 HIS 0.005 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00298 (18759) covalent geometry : angle 0.54145 (25484) SS BOND : bond 0.00441 ( 41) SS BOND : angle 1.48777 ( 82) hydrogen bonds : bond 0.04351 ( 461) hydrogen bonds : angle 4.61405 ( 1236) link_ALPHA1-2 : bond 0.00325 ( 1) link_ALPHA1-2 : angle 1.48700 ( 3) link_ALPHA1-3 : bond 0.01383 ( 7) link_ALPHA1-3 : angle 1.85380 ( 21) link_ALPHA1-6 : bond 0.02171 ( 7) link_ALPHA1-6 : angle 2.93582 ( 21) link_BETA1-4 : bond 0.00421 ( 45) link_BETA1-4 : angle 1.55144 ( 135) link_BETA1-6 : bond 0.00351 ( 2) link_BETA1-6 : angle 1.29763 ( 6) link_NAG-ASN : bond 0.00240 ( 48) link_NAG-ASN : angle 2.07731 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8074 (m110) cc_final: 0.7676 (t0) REVERT: C 95 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8487 (ptm) REVERT: C 169 ARG cc_start: 0.8371 (mmt-90) cc_final: 0.7538 (mtm-85) REVERT: G 328 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7480 (mtm-85) REVERT: M 66 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7262 (ptm160) REVERT: N 12 SER cc_start: 0.7922 (p) cc_final: 0.7655 (t) REVERT: E 79 TYR cc_start: 0.7505 (m-80) cc_final: 0.7184 (m-80) REVERT: F 77 ASP cc_start: 0.7639 (t0) cc_final: 0.7304 (t0) outliers start: 32 outliers final: 25 residues processed: 200 average time/residue: 0.1445 time to fit residues: 42.7667 Evaluate side-chains 196 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120662 restraints weight = 24812.146| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.87 r_work: 0.3297 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18910 Z= 0.161 Angle : 0.586 9.549 25896 Z= 0.277 Chirality : 0.044 0.219 3180 Planarity : 0.004 0.042 3080 Dihedral : 6.971 58.899 4542 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.80 % Allowed : 8.87 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2101 helix: 1.67 (0.27), residues: 396 sheet: 1.13 (0.21), residues: 570 loop : 0.63 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 338 TYR 0.011 0.001 TYR G 484 PHE 0.011 0.001 PHE G 159 TRP 0.017 0.001 TRP M 50 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00381 (18759) covalent geometry : angle 0.54435 (25484) SS BOND : bond 0.00437 ( 41) SS BOND : angle 1.33975 ( 82) hydrogen bonds : bond 0.04390 ( 461) hydrogen bonds : angle 4.59075 ( 1236) link_ALPHA1-2 : bond 0.00409 ( 1) link_ALPHA1-2 : angle 1.38189 ( 3) link_ALPHA1-3 : bond 0.01310 ( 7) link_ALPHA1-3 : angle 1.80966 ( 21) link_ALPHA1-6 : bond 0.02143 ( 7) link_ALPHA1-6 : angle 2.91081 ( 21) link_BETA1-4 : bond 0.00417 ( 45) link_BETA1-4 : angle 1.54970 ( 135) link_BETA1-6 : bond 0.00222 ( 2) link_BETA1-6 : angle 1.37134 ( 6) link_NAG-ASN : bond 0.00296 ( 48) link_NAG-ASN : angle 2.06158 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: C 169 ARG cc_start: 0.8374 (mmt-90) cc_final: 0.7395 (mtm-85) REVERT: G 328 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7342 (mtm-85) REVERT: M 66 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7045 (ptm160) REVERT: N 12 SER cc_start: 0.7976 (p) cc_final: 0.7678 (t) REVERT: E 79 TYR cc_start: 0.7538 (m-80) cc_final: 0.7193 (m-80) REVERT: F 77 ASP cc_start: 0.7429 (t0) cc_final: 0.7087 (t0) outliers start: 34 outliers final: 30 residues processed: 198 average time/residue: 0.1256 time to fit residues: 37.0827 Evaluate side-chains 198 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 51 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 162 optimal weight: 0.0570 chunk 190 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 130 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127135 restraints weight = 24623.892| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.68 r_work: 0.3397 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18910 Z= 0.112 Angle : 0.543 9.446 25896 Z= 0.257 Chirality : 0.043 0.201 3180 Planarity : 0.003 0.043 3080 Dihedral : 6.668 59.864 4542 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.58 % Allowed : 9.35 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.18), residues: 2101 helix: 1.90 (0.27), residues: 396 sheet: 1.16 (0.21), residues: 576 loop : 0.60 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 42 TYR 0.011 0.001 TYR C 191 PHE 0.012 0.001 PHE G 53 TRP 0.014 0.001 TRP M 50 HIS 0.003 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00247 (18759) covalent geometry : angle 0.50316 (25484) SS BOND : bond 0.00427 ( 41) SS BOND : angle 1.13484 ( 82) hydrogen bonds : bond 0.03950 ( 461) hydrogen bonds : angle 4.39498 ( 1236) link_ALPHA1-2 : bond 0.00409 ( 1) link_ALPHA1-2 : angle 1.36950 ( 3) link_ALPHA1-3 : bond 0.01368 ( 7) link_ALPHA1-3 : angle 1.85947 ( 21) link_ALPHA1-6 : bond 0.02187 ( 7) link_ALPHA1-6 : angle 2.91693 ( 21) link_BETA1-4 : bond 0.00428 ( 45) link_BETA1-4 : angle 1.48078 ( 135) link_BETA1-6 : bond 0.00375 ( 2) link_BETA1-6 : angle 1.29941 ( 6) link_NAG-ASN : bond 0.00208 ( 48) link_NAG-ASN : angle 1.89829 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.474 Fit side-chains REVERT: C 117 LYS cc_start: 0.8432 (tppt) cc_final: 0.8044 (tptp) REVERT: C 169 ARG cc_start: 0.8357 (mmt-90) cc_final: 0.7378 (mtm-85) REVERT: G 328 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7327 (mtm-85) REVERT: M 66 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7241 (ptm160) REVERT: M 72 GLU cc_start: 0.8098 (pt0) cc_final: 0.7877 (pt0) REVERT: M 100 TRP cc_start: 0.8443 (p-90) cc_final: 0.8217 (p-90) REVERT: N 12 SER cc_start: 0.7934 (p) cc_final: 0.7671 (t) REVERT: E 79 TYR cc_start: 0.7568 (m-80) cc_final: 0.7303 (m-80) REVERT: F 77 ASP cc_start: 0.7421 (t0) cc_final: 0.7074 (t70) outliers start: 30 outliers final: 28 residues processed: 193 average time/residue: 0.1284 time to fit residues: 37.2380 Evaluate side-chains 194 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 51 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN G 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.160261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126069 restraints weight = 24541.972| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.78 r_work: 0.3374 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18910 Z= 0.142 Angle : 0.561 9.498 25896 Z= 0.266 Chirality : 0.043 0.203 3180 Planarity : 0.004 0.042 3080 Dihedral : 6.565 59.674 4542 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.90 % Allowed : 9.24 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.18), residues: 2101 helix: 1.89 (0.27), residues: 396 sheet: 1.14 (0.21), residues: 576 loop : 0.56 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 42 TYR 0.010 0.001 TYR C 191 PHE 0.010 0.001 PHE G 53 TRP 0.017 0.001 TRP M 50 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00334 (18759) covalent geometry : angle 0.52125 (25484) SS BOND : bond 0.00394 ( 41) SS BOND : angle 1.28810 ( 82) hydrogen bonds : bond 0.04104 ( 461) hydrogen bonds : angle 4.43418 ( 1236) link_ALPHA1-2 : bond 0.00461 ( 1) link_ALPHA1-2 : angle 1.34042 ( 3) link_ALPHA1-3 : bond 0.01322 ( 7) link_ALPHA1-3 : angle 1.84704 ( 21) link_ALPHA1-6 : bond 0.02154 ( 7) link_ALPHA1-6 : angle 2.90813 ( 21) link_BETA1-4 : bond 0.00426 ( 45) link_BETA1-4 : angle 1.48988 ( 135) link_BETA1-6 : bond 0.00266 ( 2) link_BETA1-6 : angle 1.32995 ( 6) link_NAG-ASN : bond 0.00261 ( 48) link_NAG-ASN : angle 1.91676 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.631 Fit side-chains REVERT: C 117 LYS cc_start: 0.8409 (tppt) cc_final: 0.8036 (tptp) REVERT: C 169 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.7392 (mtm-85) REVERT: D 530 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7714 (ptm) REVERT: G 46 ARG cc_start: 0.8444 (ptm160) cc_final: 0.8006 (ptt180) REVERT: G 328 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7331 (mtm-85) REVERT: M 66 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7236 (ptm160) REVERT: M 100 TRP cc_start: 0.8517 (p-90) cc_final: 0.8258 (p-90) REVERT: N 12 SER cc_start: 0.7987 (p) cc_final: 0.7693 (t) REVERT: E 79 TYR cc_start: 0.7548 (m-80) cc_final: 0.7303 (m-80) REVERT: E 80 MET cc_start: 0.7421 (ttp) cc_final: 0.7038 (ttp) REVERT: F 77 ASP cc_start: 0.7402 (t0) cc_final: 0.7090 (t70) outliers start: 36 outliers final: 30 residues processed: 189 average time/residue: 0.1306 time to fit residues: 37.3317 Evaluate side-chains 194 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 207 optimal weight: 0.0670 chunk 34 optimal weight: 0.0570 chunk 97 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.161963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127380 restraints weight = 24533.581| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.76 r_work: 0.3404 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18910 Z= 0.110 Angle : 0.535 9.458 25896 Z= 0.253 Chirality : 0.042 0.205 3180 Planarity : 0.003 0.049 3080 Dihedral : 6.323 59.611 4542 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.80 % Allowed : 9.19 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.18), residues: 2101 helix: 2.02 (0.27), residues: 396 sheet: 1.27 (0.21), residues: 570 loop : 0.55 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 42 TYR 0.010 0.001 TYR C 191 PHE 0.010 0.001 PHE G 53 TRP 0.016 0.001 TRP M 50 HIS 0.002 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00243 (18759) covalent geometry : angle 0.49501 (25484) SS BOND : bond 0.00480 ( 41) SS BOND : angle 1.27421 ( 82) hydrogen bonds : bond 0.03835 ( 461) hydrogen bonds : angle 4.31162 ( 1236) link_ALPHA1-2 : bond 0.00425 ( 1) link_ALPHA1-2 : angle 1.37889 ( 3) link_ALPHA1-3 : bond 0.01300 ( 7) link_ALPHA1-3 : angle 1.88170 ( 21) link_ALPHA1-6 : bond 0.02141 ( 7) link_ALPHA1-6 : angle 2.90991 ( 21) link_BETA1-4 : bond 0.00425 ( 45) link_BETA1-4 : angle 1.45158 ( 135) link_BETA1-6 : bond 0.00359 ( 2) link_BETA1-6 : angle 1.27175 ( 6) link_NAG-ASN : bond 0.00206 ( 48) link_NAG-ASN : angle 1.82266 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.676 Fit side-chains REVERT: C 117 LYS cc_start: 0.8384 (tppt) cc_final: 0.8056 (tptp) REVERT: C 169 ARG cc_start: 0.8346 (mmt-90) cc_final: 0.7375 (mtm-85) REVERT: D 530 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7679 (ptm) REVERT: G 46 ARG cc_start: 0.8442 (ptm160) cc_final: 0.8010 (ptt180) REVERT: G 328 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7322 (mtm-85) REVERT: M 66 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7257 (ptm160) REVERT: M 100 TRP cc_start: 0.8433 (p-90) cc_final: 0.8185 (p-90) REVERT: N 12 SER cc_start: 0.8023 (p) cc_final: 0.7742 (t) REVERT: N 54 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7212 (mtm-85) REVERT: E 79 TYR cc_start: 0.7542 (m-80) cc_final: 0.7307 (m-80) REVERT: E 80 MET cc_start: 0.7363 (ttp) cc_final: 0.6988 (ttp) REVERT: F 77 ASP cc_start: 0.7393 (t0) cc_final: 0.7105 (t70) outliers start: 34 outliers final: 28 residues processed: 189 average time/residue: 0.1364 time to fit residues: 39.2086 Evaluate side-chains 189 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 141 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 425 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.154533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119709 restraints weight = 24837.208| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.81 r_work: 0.3249 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18910 Z= 0.164 Angle : 0.570 9.414 25896 Z= 0.271 Chirality : 0.044 0.204 3180 Planarity : 0.004 0.047 3080 Dihedral : 6.352 59.423 4542 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.69 % Allowed : 9.30 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 2101 helix: 1.69 (0.27), residues: 414 sheet: 1.15 (0.21), residues: 576 loop : 0.58 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 504 TYR 0.011 0.001 TYR G 484 PHE 0.011 0.001 PHE G 159 TRP 0.018 0.001 TRP M 50 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00393 (18759) covalent geometry : angle 0.53015 (25484) SS BOND : bond 0.00459 ( 41) SS BOND : angle 1.45293 ( 82) hydrogen bonds : bond 0.04206 ( 461) hydrogen bonds : angle 4.42858 ( 1236) link_ALPHA1-2 : bond 0.00487 ( 1) link_ALPHA1-2 : angle 1.31954 ( 3) link_ALPHA1-3 : bond 0.01238 ( 7) link_ALPHA1-3 : angle 1.85686 ( 21) link_ALPHA1-6 : bond 0.02109 ( 7) link_ALPHA1-6 : angle 2.88355 ( 21) link_BETA1-4 : bond 0.00417 ( 45) link_BETA1-4 : angle 1.48831 ( 135) link_BETA1-6 : bond 0.00226 ( 2) link_BETA1-6 : angle 1.36250 ( 6) link_NAG-ASN : bond 0.00278 ( 48) link_NAG-ASN : angle 1.90862 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.02 seconds wall clock time: 67 minutes 47.19 seconds (4067.19 seconds total)