Starting phenix.real_space_refine on Sun Sep 13 00:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.map" model { file = "/net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dcq_7858/09_2026/6dcq_7858.cif" } resolution = 3.1 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= -0.000 sd= 0.008 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 110 5.16 5 C 12064 2.51 5 N 3154 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19300 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3403 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 435, 3403 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 5 bond proxies already assigned to first conformer: 3458 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3538 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 452, 3538 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 bond proxies already assigned to first conformer: 3592 Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1167 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain: "E" Number of atoms: 3536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 448, 3515 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 448, 3515 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain breaks: 4 bond proxies already assigned to first conformer: 3563 Chain: "F" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1095 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1050 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "L" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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 chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "g" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 2 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 chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" 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 chiralities: 7 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "r" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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 chiralities: 3 Chain: "C" 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 chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS A 173 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 173 " occ=0.50 residue: pdb=" N AHIS E 173 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 173 " occ=0.50 residue: pdb=" N AARG E 444 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 444 " occ=0.50 Time building chain proxies: 5.58, per 1000 atoms: 0.29 Number of scatterers: 19300 At special positions: 0 Unit cell: (152.44, 133.9, 128.75, 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 110 16.00 O 3972 8.00 N 3154 7.00 C 12064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 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 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.23 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 9 " " BMA g 3 " - " MAN g 4 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 7 " " BMA k 3 " - " MAN k 6 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " BETA1-2 " MAN f 4 " - " NAG f 5 " " MAN g 4 " - " NAG g 5 " " MAN g 7 " - " NAG g 8 " " MAN r 4 " - " NAG r 5 " " MAN r 7 " - " NAG r 8 " " MAN s 4 " - " NAG s 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG f 5 " - " GAL f 6 " " NAG f 7 " - " GAL f 8 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " MAN g 4 " - " NAG g 6 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " 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 m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " MAN r 4 " - " NAG r 6 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG s 5 " - " GAL s 6 " " NAG s 7 " - " GAL s 8 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG f 1 " - " FUC f 10 " " MAN f 4 " - " NAG f 7 " " NAG g 1 " - " FUC g 9 " " NAG r 1 " - " FUC r 9 " " NAG s 1 " - " FUC s 9 " " MAN s 4 " - " NAG s 7 " NAG-ASN " NAG A 607 " - " ASN A 448 " " NAG A 612 " - " ASN A 234 " " NAG A 617 " - " ASN A 356 " " NAG A 628 " - " ASN A 301 " " NAG B1000 " - " ASN B 616 " " NAG B1003 " - " ASN B 637 " " NAG B1004 " - " ASN B 625 " " NAG C 601 " - " ASN C 356 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 276 " " NAG C 613 " - " ASN C 234 " " NAG C 614 " - " ASN C 88 " " NAG D1019 " - " ASN D 616 " " NAG D1020 " - " ASN D 625 " " NAG E 618 " - " ASN E 356 " " NAG E 619 " - " ASN E 88 " " NAG E 620 " - " ASN E 392 " " NAG E 623 " - " ASN E 234 " " NAG E 630 " - " ASN E 197 " " NAG F 901 " - " ASN F 625 " " NAG F 902 " - " ASN F 616 " " NAG G 1 " - " ASN A 197 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 130 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 88 " " NAG R 1 " - " ASN A 392 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 130 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN C 262 " " NAG d 1 " - " ASN C 301 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN D 611 " " NAG g 1 " - " ASN D 637 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 301 " " NAG j 1 " - " ASN E 156 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 448 " " NAG m 1 " - " ASN E 332 " " NAG n 1 " - " ASN E 386 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 160 " " NAG r 1 " - " ASN F 637 " " NAG s 1 " - " ASN F 611 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 910.3 milliseconds 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 42 sheets defined 17.7% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.122A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.849A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.558A pdb=" N LEU A 181 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.573A pdb=" N GLU A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.738A pdb=" N SER A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.869A pdb=" N LEU B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.319A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 536 through 542' Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.626A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.812A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.700A pdb=" N GLN B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 4.137A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 3.542A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 336 through 350 removed outlier: 3.575A pdb=" N ALA C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.672A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.703A pdb=" N SER C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.639A pdb=" N GLN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 565 removed outlier: 3.757A pdb=" N LEU D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 591 removed outlier: 3.695A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.753A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 628 through 636 removed outlier: 4.001A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 660 removed outlier: 3.635A pdb=" N TYR D 644 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.575A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.745A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.590A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.127A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.672A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.096A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.708A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 631 through 636 Processing helix chain 'F' and resid 638 through 660 removed outlier: 3.581A pdb=" N LEU F 645 " --> pdb=" O THR F 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 3.565A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.924A 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: 4.413A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.683A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.805A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.013A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 334 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.377A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 7.143A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.147A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.709A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.507A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.836A pdb=" N HIS C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.923A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.519A pdb=" N CYS C 131 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AB9, first strand: chain 'C' and resid 358 through 361 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 358 through 361 current: chain 'C' and resid 441 through 456 removed outlier: 6.163A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.163A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY C 441 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.133A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N ILE C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL C 286 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 315 through 323 removed outlier: 3.839A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 334 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.302A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.980A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 66 through 67 removed outlier: 7.472A pdb=" N HIS E 66 " --> pdb=" O SER E 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.514A pdb=" N CYS E 131 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.591A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.078A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 394 through 395 removed outlier: 5.947A pdb=" N THR E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE E 468 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY E 441 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 298 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 377 removed outlier: 4.529A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER E 334 " --> pdb=" O ARG E 293 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 298 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY E 441 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AD5, first strand: chain 'F' and resid 513 through 518 removed outlier: 3.527A pdb=" N GLY F 514 " --> pdb=" O TYR M 100M" (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN M 100K" --> pdb=" O GLY F 516 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG M 100J" --> pdb=" O ASP M 100E" (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.551A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.647A pdb=" N VAL H 37 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.149A pdb=" N GLU L 50 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR L 34 " --> pdb=" O MET L 89 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET L 89 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AE3, first strand: chain 'M' and resid 3 through 7 removed outlier: 4.470A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL M 18 " --> pdb=" O MET M 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET M 82 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.515A pdb=" N ALA M 93 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.723A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL N 63 " --> pdb=" O ARG N 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.669A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 86 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5900 1.34 - 1.47: 5255 1.47 - 1.60: 8366 1.60 - 1.73: 0 1.73 - 1.86: 149 Bond restraints: 19670 Sorted by residual: bond pdb=" C VAL E 411 " pdb=" N PRO E 411B" ideal model delta sigma weight residual 1.334 1.391 -0.058 8.40e-03 1.42e+04 4.73e+01 bond pdb=" C PHE C 468 " pdb=" N ARG C 469 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.26e+00 bond pdb=" CA ASN E 295 " pdb=" CB ASN E 295 " ideal model delta sigma weight residual 1.533 1.598 -0.065 2.29e-02 1.91e+03 7.96e+00 bond pdb=" C1 NAG E 620 " pdb=" O5 NAG E 620 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 19665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 25044 2.02 - 4.05: 1369 4.05 - 6.07: 206 6.07 - 8.09: 61 8.09 - 10.12: 14 Bond angle restraints: 26694 Sorted by residual: angle pdb=" C ASN E 295 " pdb=" CA ASN E 295 " pdb=" CB ASN E 295 " ideal model delta sigma weight residual 109.37 117.92 -8.55 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR H 107 " pdb=" N THR H 108 " pdb=" CA THR H 108 " ideal model delta sigma weight residual 122.82 129.08 -6.26 1.42e+00 4.96e-01 1.94e+01 angle pdb=" C LYS A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta sigma weight residual 121.97 129.91 -7.94 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C TRP F 628 " pdb=" N LEU F 629 " pdb=" CA LEU F 629 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C VAL E 505 " pdb=" N VAL E 506 " pdb=" CA VAL E 506 " ideal model delta sigma weight residual 121.70 129.12 -7.42 1.80e+00 3.09e-01 1.70e+01 ... (remaining 26689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 10206 15.13 - 30.26: 444 30.26 - 45.39: 104 45.39 - 60.52: 31 60.52 - 75.65: 9 Dihedral angle restraints: 10794 sinusoidal: 4357 harmonic: 6437 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -161.26 75.26 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.59 -61.59 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 157 " pdb=" CB CYS E 157 " ideal model delta sinusoidal sigma weight residual 93.00 37.87 55.13 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 10791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 3349 0.197 - 0.394: 37 0.394 - 0.591: 7 0.591 - 0.789: 0 0.789 - 0.986: 1 Chirality restraints: 3394 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 332 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 3391 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 479 " -0.022 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP E 479 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 479 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 479 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 479 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 479 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 479 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 479 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 479 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 479 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 356 " -0.031 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN E 356 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN E 356 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 356 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG E 618 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 93 " -0.025 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE A 93 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 93 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 93 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 93 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 93 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 93 " -0.004 2.00e-02 2.50e+03 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 48 2.43 - 3.05: 11311 3.05 - 3.67: 25997 3.67 - 4.28: 40820 4.28 - 4.90: 67113 Nonbonded interactions: 145289 Sorted by model distance: nonbonded pdb=" OE1 GLU C 335 " pdb=" C ASN C 411C" model vdw 1.817 3.270 nonbonded pdb=" OE1 GLU C 335 " pdb=" CB ASN C 411C" model vdw 1.855 3.440 nonbonded pdb=" OE1 GLU C 335 " pdb=" CA ASN C 411C" model vdw 1.964 3.470 nonbonded pdb=" OE1 GLU C 335 " pdb=" O ASN C 411C" model vdw 1.989 3.040 nonbonded pdb=" ND2 ASN E 130 " pdb=" O5 NAG q 1 " model vdw 2.072 3.120 ... (remaining 145284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 165 or resid 167 through 172 or resid 174 throu \ gh 185 or resid 188 through 443 or resid 445 through 457 or resid 464 through 50 \ 6 or resid 607 through 628)) selection = (chain 'C' and (resid 32 through 58 or resid 71 through 136 or resid 147 through \ 165 or resid 167 through 172 or resid 174 through 398 or resid 411 through 443 \ or resid 445 through 457 or resid 464 through 506 or resid 611 through 614)) selection = (chain 'E' and (resid 32 through 58 or resid 71 through 136 or resid 147 through \ 165 or resid 167 through 172 or resid 174 through 185 or resid 188 through 443 \ or resid 445 through 457 or resid 464 through 506 or resid 619 through 630)) } ncs_group { reference = (chain 'B' and (resid 512 through 655 or resid 1003 through 1004)) selection = (chain 'F' and (resid 512 through 549 or resid 572 through 655 or resid 901 thro \ ugh 902)) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) } ncs_group { reference = chain 'H' selection = (chain 'M' and resid 2 through 111) } ncs_group { reference = (chain 'L' and resid 2 through 105) selection = (chain 'N' and resid 2 through 105) } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'k' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'f' and (resid 2 or resid 10)) selection = (chain 'g' and (resid 1 or resid 9)) selection = (chain 'r' and (resid 1 or resid 9)) selection = (chain 's' and (resid 1 or resid 9)) } 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=0.50 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: 3.120 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.130 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.008 0.199 19841 Z= 0.372 Angle : 1.168 17.895 27158 Z= 0.556 Chirality : 0.071 0.986 3394 Planarity : 0.007 0.069 3203 Dihedral : 9.641 75.650 6544 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.34 % Favored : 91.56 % Rotamer: Outliers : 0.36 % Allowed : 1.99 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.14), residues: 2192 helix: -4.37 (0.11), residues: 364 sheet: -2.55 (0.19), residues: 573 loop : -2.69 (0.14), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 298 TYR 0.038 0.003 TYR C 191 PHE 0.057 0.005 PHE A 93 TRP 0.057 0.005 TRP E 479 HIS 0.013 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.37 (19670) covalent geometry : angle 1.07289 / 0.54 (26694) SS BOND : bond 0.03465 / 1.09 ( 34) SS BOND : angle 1.99723 / 1.58 ( 68) hydrogen bonds : bond 0.30669 / 20.99 ( 481) hydrogen bonds : angle 10.71677 / 7.22 ( 1393) Misc. bond : bond 0.00206 / 0.10 ( 5) link_ALPHA1-2 : bond 0.00572 / 0.29 ( 2) link_ALPHA1-2 : angle 2.68650 / 2.28 ( 6) link_ALPHA1-3 : bond 0.00680 / 0.35 ( 7) link_ALPHA1-3 : angle 2.34603 / 1.61 ( 21) link_ALPHA1-6 : bond 0.00254 / 0.13 ( 7) link_ALPHA1-6 : angle 1.70124 / 1.20 ( 21) link_BETA1-2 : bond 0.00587 / 0.28 ( 6) link_BETA1-2 : angle 1.49053 / 0.99 ( 18) link_BETA1-4 : bond 0.00895 / 0.50 ( 47) link_BETA1-4 : angle 3.05540 / 2.16 ( 141) link_BETA1-6 : bond 0.00554 / 0.27 ( 8) link_BETA1-6 : angle 1.68320 / 1.09 ( 24) link_NAG-ASN : bond 0.00759 / 0.48 ( 55) link_NAG-ASN : angle 5.14978 / 3.39 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 467 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7290 (t0) cc_final: 0.7030 (t70) REVERT: B 513 VAL cc_start: 0.9002 (t) cc_final: 0.8731 (m) REVERT: B 639 THR cc_start: 0.9013 (m) cc_final: 0.8808 (p) REVERT: C 426 MET cc_start: 0.8357 (tpt) cc_final: 0.8123 (tpt) REVERT: D 657 GLU cc_start: 0.8116 (pp20) cc_final: 0.7883 (pp20) REVERT: E 330 TYR cc_start: 0.8645 (p90) cc_final: 0.8415 (p90) REVERT: F 633 LYS cc_start: 0.8781 (mttt) cc_final: 0.8531 (mptt) REVERT: H 23 VAL cc_start: 0.7240 (t) cc_final: 0.6962 (m) REVERT: L 4 MET cc_start: 0.7686 (mmm) cc_final: 0.7355 (mmp) REVERT: L 92 LYS cc_start: 0.8873 (tmtm) cc_final: 0.8608 (tttm) REVERT: M 13 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7308 (mp10) REVERT: M 53 ASP cc_start: 0.7878 (t0) cc_final: 0.7606 (t0) REVERT: N 75 ILE cc_start: 0.8464 (mt) cc_final: 0.8144 (mt) REVERT: N 83 VAL cc_start: 0.8970 (m) cc_final: 0.8658 (t) outliers start: 5 outliers final: 0 residues processed: 470 average time/residue: 0.1648 time to fit residues: 112.8415 Evaluate side-chains 275 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN A 276 ASN A 352 HIS A 411CASN A 425 ASN A 478 ASN B 619 GLN C 103 GLN C 146 ASN C 216 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 540 GLN D 552 GLN D 607 ASN D 656 ASN E 32 ASN E 103 GLN E 187 ASN E 280 ASN E 348 GLN E 432 GLN F 540 GLN F 575 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN N 6 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108185 restraints weight = 79925.719| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 4.83 r_work: 0.3209 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 19841 Z= 0.231 Angle : 0.883 15.668 27158 Z= 0.421 Chirality : 0.052 0.454 3394 Planarity : 0.006 0.061 3203 Dihedral : 5.990 37.021 2400 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.04 % Allowed : 7.81 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.15), residues: 2192 helix: -2.38 (0.21), residues: 371 sheet: -2.00 (0.20), residues: 581 loop : -2.34 (0.15), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 444 TYR 0.025 0.002 TYR C 191 PHE 0.029 0.003 PHE N 49 TRP 0.031 0.002 TRP A 479 HIS 0.006 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (19670) covalent geometry : angle 0.80288 / 0.40 (26694) SS BOND : bond 0.00988 / 0.48 ( 34) SS BOND : angle 2.34272 / 1.49 ( 68) hydrogen bonds : bond 0.06521 / 4.45 ( 481) hydrogen bonds : angle 6.59516 / 4.43 ( 1393) Misc. bond : bond 0.00051 / 0.03 ( 5) link_ALPHA1-2 : bond 0.00559 / 0.29 ( 2) link_ALPHA1-2 : angle 1.93278 / 1.56 ( 6) link_ALPHA1-3 : bond 0.00816 / 0.42 ( 7) link_ALPHA1-3 : angle 1.65495 / 1.20 ( 21) link_ALPHA1-6 : bond 0.00497 / 0.25 ( 7) link_ALPHA1-6 : angle 1.45192 / 0.98 ( 21) link_BETA1-2 : bond 0.00226 / 0.11 ( 6) link_BETA1-2 : angle 1.42263 / 1.03 ( 18) link_BETA1-4 : bond 0.00509 / 0.32 ( 47) link_BETA1-4 : angle 1.98541 / 1.43 ( 141) link_BETA1-6 : bond 0.00425 / 0.21 ( 8) link_BETA1-6 : angle 1.42377 / 0.92 ( 24) link_NAG-ASN : bond 0.00553 / 0.33 ( 55) link_NAG-ASN : angle 4.13501 / 2.73 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8576 (tpp) cc_final: 0.8332 (tpp) REVERT: B 513 VAL cc_start: 0.9106 (t) cc_final: 0.8888 (m) REVERT: B 621 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8019 (tm-30) REVERT: C 378 CYS cc_start: 0.7118 (t) cc_final: 0.6734 (t) REVERT: C 426 MET cc_start: 0.8780 (tpt) cc_final: 0.8463 (tpt) REVERT: C 432 GLN cc_start: 0.8439 (mt0) cc_final: 0.8138 (mp10) REVERT: E 72 HIS cc_start: 0.7662 (p90) cc_final: 0.7309 (p-80) REVERT: E 107 ASP cc_start: 0.8503 (m-30) cc_final: 0.8276 (m-30) REVERT: F 545 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9043 (tp) REVERT: H 91 ARG cc_start: 0.7435 (mmt90) cc_final: 0.7229 (mmt90) REVERT: M 13 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7449 (mp10) REVERT: M 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7862 (t0) REVERT: N 24 LYS cc_start: 0.8252 (tptt) cc_final: 0.7408 (mtmm) REVERT: N 39 LYS cc_start: 0.7554 (mmtt) cc_final: 0.7094 (mmtt) REVERT: N 82 ASP cc_start: 0.7318 (m-30) cc_final: 0.7103 (m-30) outliers start: 38 outliers final: 24 residues processed: 323 average time/residue: 0.1506 time to fit residues: 73.0377 Evaluate side-chains 295 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 2 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN C 72 HIS C 374 HIS D 656 ASN E 32 ASN E 195 ASN E 374 HIS E 478 ASN F 540 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106056 restraints weight = 91871.460| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.68 r_work: 0.3206 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19841 Z= 0.159 Angle : 0.780 14.518 27158 Z= 0.367 Chirality : 0.049 0.374 3394 Planarity : 0.005 0.058 3203 Dihedral : 5.528 42.972 2400 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.04 % Allowed : 9.44 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.16), residues: 2192 helix: -1.16 (0.25), residues: 369 sheet: -1.79 (0.20), residues: 586 loop : -2.02 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 46 TYR 0.022 0.002 TYR C 191 PHE 0.024 0.002 PHE N 49 TRP 0.016 0.001 TRP E 338 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (19670) covalent geometry : angle 0.70503 / 0.35 (26694) SS BOND : bond 0.00577 / 0.29 ( 34) SS BOND : angle 2.21347 / 1.47 ( 68) hydrogen bonds : bond 0.04842 / 3.33 ( 481) hydrogen bonds : angle 5.84631 / 3.92 ( 1393) Misc. bond : bond 0.00039 / 0.02 ( 5) link_ALPHA1-2 : bond 0.00528 / 0.28 ( 2) link_ALPHA1-2 : angle 1.81278 / 1.42 ( 6) link_ALPHA1-3 : bond 0.00724 / 0.38 ( 7) link_ALPHA1-3 : angle 1.62387 / 1.13 ( 21) link_ALPHA1-6 : bond 0.00497 / 0.25 ( 7) link_ALPHA1-6 : angle 1.37931 / 0.95 ( 21) link_BETA1-2 : bond 0.00210 / 0.10 ( 6) link_BETA1-2 : angle 1.29690 / 0.95 ( 18) link_BETA1-4 : bond 0.00491 / 0.31 ( 47) link_BETA1-4 : angle 1.78365 / 1.29 ( 141) link_BETA1-6 : bond 0.00371 / 0.18 ( 8) link_BETA1-6 : angle 1.24851 / 0.82 ( 24) link_NAG-ASN : bond 0.00493 / 0.30 ( 55) link_NAG-ASN : angle 3.73981 / 2.48 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9294 (mt) cc_final: 0.9000 (pt) REVERT: A 446 ASP cc_start: 0.7914 (m-30) cc_final: 0.7448 (m-30) REVERT: B 513 VAL cc_start: 0.9097 (t) cc_final: 0.8875 (m) REVERT: B 621 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8082 (tm-30) REVERT: B 647 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8181 (tm-30) REVERT: C 368 ASP cc_start: 0.7788 (p0) cc_final: 0.7587 (p0) REVERT: C 378 CYS cc_start: 0.7225 (t) cc_final: 0.6871 (t) REVERT: C 426 MET cc_start: 0.8692 (tpt) cc_final: 0.8418 (tpt) REVERT: C 432 GLN cc_start: 0.8455 (mt0) cc_final: 0.8228 (mp10) REVERT: E 72 HIS cc_start: 0.7574 (p90) cc_final: 0.7256 (p-80) REVERT: E 486 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7267 (p90) REVERT: F 545 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9042 (tp) REVERT: H 30 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8960 (t) REVERT: M 13 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7443 (mp10) REVERT: M 53 ASP cc_start: 0.8185 (t0) cc_final: 0.7803 (t0) REVERT: N 24 LYS cc_start: 0.8239 (tptt) cc_final: 0.7417 (mtmm) REVERT: N 74 ARG cc_start: 0.8252 (tmt-80) cc_final: 0.7944 (tmt170) outliers start: 38 outliers final: 25 residues processed: 310 average time/residue: 0.1530 time to fit residues: 70.9584 Evaluate side-chains 291 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 202 optimal weight: 0.3980 chunk 156 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 76 optimal weight: 0.0370 chunk 139 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS D 656 ASN F 619 GLN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.141691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108983 restraints weight = 85967.540| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.41 r_work: 0.3229 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19841 Z= 0.134 Angle : 0.727 14.285 27158 Z= 0.337 Chirality : 0.047 0.337 3394 Planarity : 0.005 0.083 3203 Dihedral : 5.147 35.260 2400 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.04 % Allowed : 10.77 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.17), residues: 2192 helix: -0.54 (0.27), residues: 369 sheet: -1.44 (0.20), residues: 588 loop : -1.83 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 293 TYR 0.021 0.001 TYR C 191 PHE 0.021 0.002 PHE N 49 TRP 0.013 0.001 TRP E 338 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (19670) covalent geometry : angle 0.66031 / 0.32 (26694) SS BOND : bond 0.00572 / 0.28 ( 34) SS BOND : angle 1.53531 / 0.94 ( 68) hydrogen bonds : bond 0.04131 / 2.85 ( 481) hydrogen bonds : angle 5.43377 / 3.64 ( 1393) Misc. bond : bond 0.00112 / 0.05 ( 5) link_ALPHA1-2 : bond 0.00519 / 0.27 ( 2) link_ALPHA1-2 : angle 1.76771 / 1.41 ( 6) link_ALPHA1-3 : bond 0.00694 / 0.36 ( 7) link_ALPHA1-3 : angle 1.59061 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00499 / 0.25 ( 7) link_ALPHA1-6 : angle 1.35431 / 0.94 ( 21) link_BETA1-2 : bond 0.00200 / 0.10 ( 6) link_BETA1-2 : angle 1.23670 / 0.91 ( 18) link_BETA1-4 : bond 0.00490 / 0.30 ( 47) link_BETA1-4 : angle 1.68042 / 1.22 ( 141) link_BETA1-6 : bond 0.00371 / 0.18 ( 8) link_BETA1-6 : angle 1.21872 / 0.80 ( 24) link_NAG-ASN : bond 0.00468 / 0.29 ( 55) link_NAG-ASN : angle 3.46428 / 2.31 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9312 (mt) cc_final: 0.9062 (pt) REVERT: A 475 MET cc_start: 0.8687 (tpp) cc_final: 0.8423 (tpp) REVERT: B 513 VAL cc_start: 0.9089 (t) cc_final: 0.8870 (m) REVERT: B 621 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 651 ASN cc_start: 0.8116 (m-40) cc_final: 0.7799 (m-40) REVERT: C 378 CYS cc_start: 0.7228 (t) cc_final: 0.6890 (t) REVERT: E 72 HIS cc_start: 0.7586 (p90) cc_final: 0.7222 (p-80) REVERT: E 133 ASN cc_start: 0.8397 (p0) cc_final: 0.8090 (m-40) REVERT: E 486 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7599 (p90) REVERT: F 545 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9015 (tp) REVERT: F 620 ASP cc_start: 0.8574 (t0) cc_final: 0.8362 (t0) REVERT: L 75 ILE cc_start: 0.5983 (mm) cc_final: 0.5545 (mt) REVERT: M 13 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7369 (mp10) REVERT: M 53 ASP cc_start: 0.8181 (t0) cc_final: 0.7858 (t0) REVERT: N 24 LYS cc_start: 0.8324 (tptt) cc_final: 0.7506 (mtmm) outliers start: 38 outliers final: 23 residues processed: 310 average time/residue: 0.1529 time to fit residues: 71.7151 Evaluate side-chains 294 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 83 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 73 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 179 optimal weight: 0.1980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS D 656 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.142577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108496 restraints weight = 82962.616| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.53 r_work: 0.3247 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19841 Z= 0.111 Angle : 0.689 14.397 27158 Z= 0.318 Chirality : 0.046 0.303 3394 Planarity : 0.004 0.051 3203 Dihedral : 4.828 33.051 2400 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.89 % Allowed : 11.99 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2192 helix: 0.05 (0.28), residues: 358 sheet: -1.11 (0.21), residues: 579 loop : -1.71 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 293 TYR 0.019 0.001 TYR C 191 PHE 0.025 0.002 PHE H 67 TRP 0.011 0.001 TRP E 338 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (19670) covalent geometry : angle 0.62513 / 0.30 (26694) SS BOND : bond 0.00522 / 0.24 ( 34) SS BOND : angle 1.43451 / 1.02 ( 68) hydrogen bonds : bond 0.03584 / 2.48 ( 481) hydrogen bonds : angle 5.15029 / 3.45 ( 1393) Misc. bond : bond 0.00062 / 0.03 ( 5) link_ALPHA1-2 : bond 0.00494 / 0.26 ( 2) link_ALPHA1-2 : angle 1.70488 / 1.37 ( 6) link_ALPHA1-3 : bond 0.00709 / 0.37 ( 7) link_ALPHA1-3 : angle 1.56705 / 1.09 ( 21) link_ALPHA1-6 : bond 0.00522 / 0.26 ( 7) link_ALPHA1-6 : angle 1.33582 / 0.93 ( 21) link_BETA1-2 : bond 0.00233 / 0.12 ( 6) link_BETA1-2 : angle 1.12843 / 0.83 ( 18) link_BETA1-4 : bond 0.00506 / 0.31 ( 47) link_BETA1-4 : angle 1.58415 / 1.15 ( 141) link_BETA1-6 : bond 0.00393 / 0.19 ( 8) link_BETA1-6 : angle 1.12504 / 0.75 ( 24) link_NAG-ASN : bond 0.00474 / 0.30 ( 55) link_NAG-ASN : angle 3.30815 / 2.23 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8117 (m-40) cc_final: 0.7710 (m-40) REVERT: A 446 ASP cc_start: 0.8076 (m-30) cc_final: 0.7773 (m-30) REVERT: A 475 MET cc_start: 0.8717 (tpp) cc_final: 0.8422 (tpp) REVERT: B 621 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 368 ASP cc_start: 0.7711 (p0) cc_final: 0.7395 (p0) REVERT: C 378 CYS cc_start: 0.7343 (t) cc_final: 0.7078 (t) REVERT: E 72 HIS cc_start: 0.7622 (p90) cc_final: 0.7232 (p-80) REVERT: E 133 ASN cc_start: 0.8295 (p0) cc_final: 0.8093 (m-40) REVERT: F 545 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9251 (tm) REVERT: H 81 GLU cc_start: 0.7425 (tp30) cc_final: 0.6938 (mm-30) REVERT: L 39 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7344 (mtpp) REVERT: L 75 ILE cc_start: 0.5567 (mm) cc_final: 0.5116 (mt) REVERT: M 13 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7272 (mp10) REVERT: M 53 ASP cc_start: 0.8172 (t0) cc_final: 0.7864 (t0) REVERT: N 24 LYS cc_start: 0.8369 (tptt) cc_final: 0.7484 (mtmm) REVERT: N 61 ARG cc_start: 0.7949 (ptm160) cc_final: 0.7691 (mtm180) REVERT: N 92 LYS cc_start: 0.8739 (tptm) cc_final: 0.8479 (tptm) outliers start: 35 outliers final: 26 residues processed: 326 average time/residue: 0.1590 time to fit residues: 77.5005 Evaluate side-chains 294 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 101 optimal weight: 0.3980 chunk 144 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS D 656 ASN F 651 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105867 restraints weight = 74894.158| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.31 r_work: 0.3216 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19841 Z= 0.148 Angle : 0.722 14.199 27158 Z= 0.334 Chirality : 0.047 0.316 3394 Planarity : 0.004 0.048 3203 Dihedral : 4.867 33.734 2400 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.35 % Allowed : 12.35 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2192 helix: 0.07 (0.28), residues: 369 sheet: -1.04 (0.21), residues: 589 loop : -1.62 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 100C TYR 0.020 0.001 TYR C 191 PHE 0.028 0.002 PHE H 67 TRP 0.013 0.001 TRP E 338 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (19670) covalent geometry : angle 0.65846 / 0.32 (26694) SS BOND : bond 0.00544 / 0.27 ( 34) SS BOND : angle 1.52466 / 1.02 ( 68) hydrogen bonds : bond 0.03890 / 2.69 ( 481) hydrogen bonds : angle 5.11292 / 3.43 ( 1393) Misc. bond : bond 0.00055 / 0.03 ( 5) link_ALPHA1-2 : bond 0.00461 / 0.24 ( 2) link_ALPHA1-2 : angle 1.71623 / 1.37 ( 6) link_ALPHA1-3 : bond 0.00654 / 0.34 ( 7) link_ALPHA1-3 : angle 1.59613 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00433 / 0.22 ( 7) link_ALPHA1-6 : angle 1.36179 / 0.94 ( 21) link_BETA1-2 : bond 0.00192 / 0.09 ( 6) link_BETA1-2 : angle 1.24316 / 0.90 ( 18) link_BETA1-4 : bond 0.00459 / 0.28 ( 47) link_BETA1-4 : angle 1.67620 / 1.21 ( 141) link_BETA1-6 : bond 0.00322 / 0.16 ( 8) link_BETA1-6 : angle 1.28950 / 0.84 ( 24) link_NAG-ASN : bond 0.00414 / 0.26 ( 55) link_NAG-ASN : angle 3.34531 / 2.24 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8176 (m-40) cc_final: 0.7714 (m-40) REVERT: A 446 ASP cc_start: 0.8114 (m-30) cc_final: 0.7848 (m-30) REVERT: B 621 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 378 CYS cc_start: 0.7295 (t) cc_final: 0.7031 (t) REVERT: E 72 HIS cc_start: 0.7628 (p90) cc_final: 0.7223 (p-80) REVERT: E 133 ASN cc_start: 0.8365 (p0) cc_final: 0.8152 (m-40) REVERT: E 199 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8480 (p) REVERT: E 486 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7443 (p90) REVERT: F 545 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9022 (tp) REVERT: H 64 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7779 (tp-100) REVERT: H 67 PHE cc_start: 0.8333 (m-80) cc_final: 0.7949 (m-80) REVERT: L 39 LYS cc_start: 0.7754 (mtpp) cc_final: 0.7403 (mtpp) REVERT: M 13 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7290 (mp10) REVERT: M 53 ASP cc_start: 0.8241 (t0) cc_final: 0.7935 (t0) REVERT: N 24 LYS cc_start: 0.8382 (tptt) cc_final: 0.7529 (mtmm) REVERT: N 61 ARG cc_start: 0.7623 (ptm160) cc_final: 0.7021 (ptp-170) REVERT: N 62 PHE cc_start: 0.7299 (m-80) cc_final: 0.6923 (m-80) REVERT: N 75 ILE cc_start: 0.7939 (mt) cc_final: 0.7721 (tt) REVERT: N 92 LYS cc_start: 0.8792 (tptm) cc_final: 0.8571 (tptm) outliers start: 44 outliers final: 33 residues processed: 289 average time/residue: 0.1495 time to fit residues: 65.2005 Evaluate side-chains 297 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 180 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 207 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS C 72 HIS D 656 ASN F 651 ASN H 13 GLN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103299 restraints weight = 100270.102| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 5.42 r_work: 0.3169 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19841 Z= 0.143 Angle : 0.723 14.145 27158 Z= 0.333 Chirality : 0.047 0.302 3394 Planarity : 0.004 0.049 3203 Dihedral : 4.936 41.202 2400 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.50 % Allowed : 12.86 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.17), residues: 2192 helix: 0.17 (0.28), residues: 369 sheet: -0.87 (0.21), residues: 570 loop : -1.58 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 100C TYR 0.020 0.001 TYR C 191 PHE 0.021 0.002 PHE H 67 TRP 0.012 0.001 TRP E 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (19670) covalent geometry : angle 0.65973 / 0.32 (26694) SS BOND : bond 0.00501 / 0.25 ( 34) SS BOND : angle 1.74531 / 1.21 ( 68) hydrogen bonds : bond 0.03795 / 2.62 ( 481) hydrogen bonds : angle 5.04545 / 3.38 ( 1393) Misc. bond : bond 0.00052 / 0.03 ( 5) link_ALPHA1-2 : bond 0.00589 / 0.30 ( 2) link_ALPHA1-2 : angle 1.75763 / 1.41 ( 6) link_ALPHA1-3 : bond 0.00658 / 0.34 ( 7) link_ALPHA1-3 : angle 1.59118 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00446 / 0.22 ( 7) link_ALPHA1-6 : angle 1.35962 / 0.94 ( 21) link_BETA1-2 : bond 0.00185 / 0.09 ( 6) link_BETA1-2 : angle 1.20104 / 0.87 ( 18) link_BETA1-4 : bond 0.00462 / 0.29 ( 47) link_BETA1-4 : angle 1.64318 / 1.18 ( 141) link_BETA1-6 : bond 0.00254 / 0.13 ( 8) link_BETA1-6 : angle 1.24346 / 0.81 ( 24) link_NAG-ASN : bond 0.00408 / 0.26 ( 55) link_NAG-ASN : angle 3.31170 / 2.22 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8212 (m-40) cc_final: 0.7754 (m-40) REVERT: B 621 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 378 CYS cc_start: 0.7494 (t) cc_final: 0.7226 (t) REVERT: E 72 HIS cc_start: 0.7665 (p90) cc_final: 0.7252 (p-80) REVERT: E 153 GLU cc_start: 0.7879 (pp20) cc_final: 0.7354 (pp20) REVERT: F 545 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9260 (tm) REVERT: H 64 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7887 (tp-100) REVERT: L 39 LYS cc_start: 0.7753 (mtpp) cc_final: 0.7373 (mtpp) REVERT: L 89 MET cc_start: 0.7105 (tpp) cc_final: 0.6499 (tpp) REVERT: M 13 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7298 (mp10) REVERT: M 53 ASP cc_start: 0.8259 (t0) cc_final: 0.7945 (t0) REVERT: N 24 LYS cc_start: 0.8374 (tptt) cc_final: 0.7526 (mtmm) REVERT: N 61 ARG cc_start: 0.7666 (ptm160) cc_final: 0.7003 (ptp-170) REVERT: N 75 ILE cc_start: 0.7896 (mt) cc_final: 0.7635 (tt) outliers start: 47 outliers final: 39 residues processed: 296 average time/residue: 0.1523 time to fit residues: 68.2570 Evaluate side-chains 300 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 123 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN C 72 HIS D 656 ASN F 577 GLN F 651 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103715 restraints weight = 88387.039| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.10 r_work: 0.3176 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19841 Z= 0.144 Angle : 0.727 14.019 27158 Z= 0.335 Chirality : 0.047 0.297 3394 Planarity : 0.004 0.048 3203 Dihedral : 4.886 36.820 2400 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.50 % Allowed : 13.16 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2192 helix: 0.26 (0.28), residues: 368 sheet: -0.83 (0.21), residues: 563 loop : -1.57 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 100C TYR 0.026 0.001 TYR C 177 PHE 0.018 0.002 PHE N 49 TRP 0.011 0.001 TRP E 338 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (19670) covalent geometry : angle 0.66435 / 0.32 (26694) SS BOND : bond 0.00510 / 0.25 ( 34) SS BOND : angle 1.83562 / 1.31 ( 68) hydrogen bonds : bond 0.03777 / 2.61 ( 481) hydrogen bonds : angle 4.97774 / 3.34 ( 1393) Misc. bond : bond 0.00052 / 0.03 ( 5) link_ALPHA1-2 : bond 0.00472 / 0.24 ( 2) link_ALPHA1-2 : angle 1.74180 / 1.39 ( 6) link_ALPHA1-3 : bond 0.00654 / 0.34 ( 7) link_ALPHA1-3 : angle 1.59209 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00443 / 0.22 ( 7) link_ALPHA1-6 : angle 1.36143 / 0.94 ( 21) link_BETA1-2 : bond 0.00188 / 0.09 ( 6) link_BETA1-2 : angle 1.21845 / 0.88 ( 18) link_BETA1-4 : bond 0.00459 / 0.28 ( 47) link_BETA1-4 : angle 1.63252 / 1.18 ( 141) link_BETA1-6 : bond 0.00333 / 0.16 ( 8) link_BETA1-6 : angle 1.27094 / 0.83 ( 24) link_NAG-ASN : bond 0.00404 / 0.25 ( 55) link_NAG-ASN : angle 3.28632 / 2.20 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8196 (m-40) cc_final: 0.7739 (m-40) REVERT: B 621 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 378 CYS cc_start: 0.7590 (t) cc_final: 0.7341 (t) REVERT: D 621 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 72 HIS cc_start: 0.7623 (p90) cc_final: 0.7207 (p-80) REVERT: E 153 GLU cc_start: 0.7847 (pp20) cc_final: 0.7193 (pp20) REVERT: F 545 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9259 (tm) REVERT: F 620 ASP cc_start: 0.8659 (t0) cc_final: 0.8398 (t0) REVERT: L 39 LYS cc_start: 0.7787 (mtpp) cc_final: 0.7417 (mtpp) REVERT: M 13 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7347 (mp10) REVERT: M 53 ASP cc_start: 0.8245 (t0) cc_final: 0.7935 (t0) REVERT: N 24 LYS cc_start: 0.8366 (tptt) cc_final: 0.7537 (mtmm) REVERT: N 61 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7089 (ptp-170) REVERT: N 75 ILE cc_start: 0.7873 (mt) cc_final: 0.7617 (tt) outliers start: 47 outliers final: 39 residues processed: 293 average time/residue: 0.1508 time to fit residues: 66.7772 Evaluate side-chains 301 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 217 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 151 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS D 656 ASN E 279 ASN F 651 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.142183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105097 restraints weight = 94405.804| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 5.32 r_work: 0.3201 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19841 Z= 0.118 Angle : 0.696 13.719 27158 Z= 0.321 Chirality : 0.046 0.283 3394 Planarity : 0.004 0.055 3203 Dihedral : 4.728 34.882 2400 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.09 % Allowed : 13.83 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.17), residues: 2192 helix: 0.42 (0.28), residues: 368 sheet: -0.83 (0.21), residues: 596 loop : -1.49 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 100C TYR 0.018 0.001 TYR C 191 PHE 0.021 0.001 PHE H 67 TRP 0.010 0.001 TRP E 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19670) covalent geometry : angle 0.63535 / 0.31 (26694) SS BOND : bond 0.00535 / 0.26 ( 34) SS BOND : angle 1.91175 / 1.27 ( 68) hydrogen bonds : bond 0.03420 / 2.36 ( 481) hydrogen bonds : angle 4.86137 / 3.27 ( 1393) Misc. bond : bond 0.00049 / 0.02 ( 5) link_ALPHA1-2 : bond 0.00444 / 0.23 ( 2) link_ALPHA1-2 : angle 1.70304 / 1.36 ( 6) link_ALPHA1-3 : bond 0.00666 / 0.35 ( 7) link_ALPHA1-3 : angle 1.58100 / 1.09 ( 21) link_ALPHA1-6 : bond 0.00484 / 0.24 ( 7) link_ALPHA1-6 : angle 1.35014 / 0.94 ( 21) link_BETA1-2 : bond 0.00217 / 0.11 ( 6) link_BETA1-2 : angle 1.13935 / 0.84 ( 18) link_BETA1-4 : bond 0.00480 / 0.29 ( 47) link_BETA1-4 : angle 1.54067 / 1.11 ( 141) link_BETA1-6 : bond 0.00360 / 0.18 ( 8) link_BETA1-6 : angle 1.16917 / 0.77 ( 24) link_NAG-ASN : bond 0.00425 / 0.27 ( 55) link_NAG-ASN : angle 3.14177 / 2.10 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8129 (m-40) cc_final: 0.7693 (m-40) REVERT: B 621 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 647 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8168 (tp30) REVERT: C 378 CYS cc_start: 0.7584 (t) cc_final: 0.7340 (t) REVERT: D 620 ASP cc_start: 0.8003 (t70) cc_final: 0.7718 (t0) REVERT: D 621 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 72 HIS cc_start: 0.7630 (p90) cc_final: 0.7198 (p-80) REVERT: E 153 GLU cc_start: 0.7768 (pp20) cc_final: 0.7161 (pp20) REVERT: F 545 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9257 (tm) REVERT: F 620 ASP cc_start: 0.8656 (t0) cc_final: 0.8400 (t0) REVERT: H 64 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8026 (tp-100) REVERT: H 81 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7386 (mm-30) REVERT: L 27 GLU cc_start: 0.6852 (mp0) cc_final: 0.6639 (mp0) REVERT: L 39 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7381 (mtpp) REVERT: M 13 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7374 (mp10) REVERT: M 53 ASP cc_start: 0.8259 (t0) cc_final: 0.7961 (t0) REVERT: N 24 LYS cc_start: 0.8358 (tptt) cc_final: 0.7568 (mtmm) REVERT: N 61 ARG cc_start: 0.7635 (ptm160) cc_final: 0.7092 (ptp-170) REVERT: N 75 ILE cc_start: 0.7842 (mt) cc_final: 0.7565 (tt) outliers start: 39 outliers final: 31 residues processed: 303 average time/residue: 0.1576 time to fit residues: 72.2422 Evaluate side-chains 304 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 93 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS D 656 ASN E 279 ASN F 575 GLN F 651 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105990 restraints weight = 87549.404| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.78 r_work: 0.3189 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19841 Z= 0.153 Angle : 0.737 13.683 27158 Z= 0.340 Chirality : 0.047 0.296 3394 Planarity : 0.004 0.052 3203 Dihedral : 4.860 35.459 2400 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.09 % Allowed : 14.03 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2192 helix: 0.40 (0.28), residues: 368 sheet: -0.77 (0.21), residues: 576 loop : -1.49 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 100C TYR 0.019 0.001 TYR C 191 PHE 0.021 0.002 PHE H 67 TRP 0.011 0.001 TRP E 338 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (19670) covalent geometry : angle 0.67417 / 0.32 (26694) SS BOND : bond 0.00568 / 0.29 ( 34) SS BOND : angle 2.31374 / 1.48 ( 68) hydrogen bonds : bond 0.03730 / 2.58 ( 481) hydrogen bonds : angle 4.89949 / 3.30 ( 1393) Misc. bond : bond 0.00050 / 0.02 ( 5) link_ALPHA1-2 : bond 0.00457 / 0.24 ( 2) link_ALPHA1-2 : angle 1.72972 / 1.38 ( 6) link_ALPHA1-3 : bond 0.00642 / 0.33 ( 7) link_ALPHA1-3 : angle 1.60962 / 1.11 ( 21) link_ALPHA1-6 : bond 0.00426 / 0.21 ( 7) link_ALPHA1-6 : angle 1.35891 / 0.94 ( 21) link_BETA1-2 : bond 0.00187 / 0.09 ( 6) link_BETA1-2 : angle 1.23098 / 0.88 ( 18) link_BETA1-4 : bond 0.00454 / 0.28 ( 47) link_BETA1-4 : angle 1.62030 / 1.17 ( 141) link_BETA1-6 : bond 0.00346 / 0.17 ( 8) link_BETA1-6 : angle 1.29286 / 0.84 ( 24) link_NAG-ASN : bond 0.00392 / 0.25 ( 55) link_NAG-ASN : angle 3.19940 / 2.14 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8159 (m-40) cc_final: 0.7733 (m-40) REVERT: B 621 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 378 CYS cc_start: 0.7591 (t) cc_final: 0.7369 (t) REVERT: D 620 ASP cc_start: 0.8043 (t70) cc_final: 0.7735 (t0) REVERT: D 621 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8098 (tm-30) REVERT: E 153 GLU cc_start: 0.7729 (pp20) cc_final: 0.7134 (pp20) REVERT: F 545 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9270 (tm) REVERT: F 620 ASP cc_start: 0.8609 (t0) cc_final: 0.8361 (t0) REVERT: H 64 GLN cc_start: 0.8320 (tp-100) cc_final: 0.8029 (tp-100) REVERT: L 27 GLU cc_start: 0.6844 (mp0) cc_final: 0.6602 (mp0) REVERT: L 39 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7428 (mtpp) REVERT: L 89 MET cc_start: 0.6995 (tpp) cc_final: 0.6467 (tpp) REVERT: M 13 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7340 (mp10) REVERT: M 53 ASP cc_start: 0.8222 (t0) cc_final: 0.7936 (t0) REVERT: N 24 LYS cc_start: 0.8323 (tptt) cc_final: 0.7556 (mtmm) REVERT: N 61 ARG cc_start: 0.7628 (ptm160) cc_final: 0.6967 (ptp-170) REVERT: N 75 ILE cc_start: 0.7899 (mt) cc_final: 0.7611 (tt) outliers start: 39 outliers final: 36 residues processed: 288 average time/residue: 0.1520 time to fit residues: 66.1066 Evaluate side-chains 304 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 172 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS D 656 ASN E 72 HIS E 279 ASN F 575 GLN F 651 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103755 restraints weight = 90615.656| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 5.18 r_work: 0.3179 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19841 Z= 0.142 Angle : 0.725 13.606 27158 Z= 0.334 Chirality : 0.046 0.291 3394 Planarity : 0.004 0.059 3203 Dihedral : 4.859 35.440 2400 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.09 % Allowed : 14.23 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2192 helix: 0.34 (0.28), residues: 374 sheet: -0.62 (0.21), residues: 566 loop : -1.49 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 304 TYR 0.024 0.001 TYR B 644 PHE 0.022 0.002 PHE H 67 TRP 0.011 0.001 TRP E 427 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (19670) covalent geometry : angle 0.66419 / 0.32 (26694) SS BOND : bond 0.00541 / 0.27 ( 34) SS BOND : angle 2.10252 / 1.37 ( 68) hydrogen bonds : bond 0.03672 / 2.54 ( 481) hydrogen bonds : angle 4.88631 / 3.29 ( 1393) Misc. bond : bond 0.00049 / 0.02 ( 5) link_ALPHA1-2 : bond 0.00451 / 0.23 ( 2) link_ALPHA1-2 : angle 1.72921 / 1.37 ( 6) link_ALPHA1-3 : bond 0.00643 / 0.33 ( 7) link_ALPHA1-3 : angle 1.59776 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00441 / 0.22 ( 7) link_ALPHA1-6 : angle 1.35409 / 0.94 ( 21) link_BETA1-2 : bond 0.00182 / 0.09 ( 6) link_BETA1-2 : angle 1.19568 / 0.87 ( 18) link_BETA1-4 : bond 0.00459 / 0.28 ( 47) link_BETA1-4 : angle 1.59457 / 1.15 ( 141) link_BETA1-6 : bond 0.00337 / 0.16 ( 8) link_BETA1-6 : angle 1.25062 / 0.82 ( 24) link_NAG-ASN : bond 0.00396 / 0.25 ( 55) link_NAG-ASN : angle 3.16948 / 2.12 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5175.90 seconds wall clock time: 89 minutes 26.84 seconds (5366.84 seconds total)