Starting phenix.real_space_refine on Sun Sep 13 21:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ozc_20224/09_2026/6ozc_20224.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 150 5.16 5 C 16083 2.51 5 N 4164 2.21 5 O 5424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 25821 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "G" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "Q" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "F" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "R" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "P" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} 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: 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: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "V" 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: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "X" 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: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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: 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: "d" 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: "e" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "f" 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: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "h" 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: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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: "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: 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: "n" 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: "o" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "p" 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: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "r" 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: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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: 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: 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: "E" 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: "G" 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: "F" 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: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.14, per 1000 atoms: 0.24 Number of scatterers: 25821 At special positions: 0 Unit cell: (188.64, 197.81, 137.55, 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 150 16.00 O 5424 8.00 N 4164 7.00 C 16083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " 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=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.07 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.12 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN W 5 " - " MAN W 6 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN c 4 " - " MAN c 5 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN g 5 " - " MAN g 6 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN m 4 " - " MAN m 5 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " " MAN q 5 " - " MAN q 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 5 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 7 " - " MAN e 8 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 8 " " MAN g 4 " - " MAN g 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 8 " " MAN i 4 " - " MAN i 5 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " MAN o 7 " - " MAN o 8 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 8 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 7 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 7 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 7 " " MAN e 7 " - " MAN e 9 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 7 " " BMA h 3 " - " MAN h 7 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 7 " " BMA m 3 " - " MAN m 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 7 " " MAN o 7 " - " MAN o 9 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 7 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 626 " - " ASN A 133 " " NAG A 653 " - " ASN A 234 " " NAG A 656 " - " ASN A 160 " " NAG A 659 " - " ASN A 197 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 626 " - " ASN E 133 " " NAG E 653 " - " ASN E 234 " " NAG E 656 " - " ASN E 160 " " NAG E 659 " - " ASN E 197 " " NAG F 626 " - " ASN F 133 " " NAG F 653 " - " ASN F 234 " " NAG F 656 " - " ASN F 160 " " NAG F 659 " - " ASN F 197 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 339 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 392 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 339 " " NAG j 1 " - " ASN E 448 " " NAG k 1 " - " ASN E 301 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN F 262 " " NAG n 1 " - " ASN F 363 " " NAG o 1 " - " ASN F 392 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 332 " " NAG r 1 " - " ASN F 295 " " NAG s 1 " - " ASN F 339 " " NAG t 1 " - " ASN F 448 " " NAG u 1 " - " ASN F 301 " " NAG v 1 " - " ASN F 156 " Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 66 sheets defined 18.1% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 4.063A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 535 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY G 572 " --> pdb=" O LEU G 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 661 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 52A through 55 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 52A through 55 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY I 572 " --> pdb=" O LEU I 568 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU I 592 " --> pdb=" O ARG I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 661 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52A through 55 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 52A through 55 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 495 through 498 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.636A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.536A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 495 through 498 Processing sheet with id=AF1, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AF2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF3, first strand: chain 'F' and resid 92 through 94 Processing sheet with id=AF4, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AF5, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 298 current: chain 'F' and resid 358 through 361 Processing sheet with id=AF7, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 443 through 456 current: chain 'F' and resid 413 through 416 Processing sheet with id=AF8, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AG1, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.663A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2421 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: 6.67 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5455 1.32 - 1.45: 8504 1.45 - 1.59: 12135 1.59 - 1.72: 21 1.72 - 1.86: 198 Bond restraints: 26313 Sorted by residual: bond pdb=" C1 NAG F 659 " pdb=" O5 NAG F 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C1 NAG A 659 " pdb=" O5 NAG A 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C1 NAG E 659 " pdb=" O5 NAG E 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C THR B 627 " pdb=" N TRP B 628 " ideal model delta sigma weight residual 1.335 1.247 0.087 1.25e-02 6.40e+03 4.90e+01 bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.20e-02 2.07e+03 4.89e+01 ... (remaining 26308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 30330 2.50 - 5.00: 4658 5.00 - 7.50: 658 7.50 - 10.00: 57 10.00 - 12.51: 9 Bond angle restraints: 35712 Sorted by residual: angle pdb=" N ARG J 66 " pdb=" CA ARG J 66 " pdb=" C ARG J 66 " ideal model delta sigma weight residual 113.88 101.37 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG C 66 " pdb=" CA ARG C 66 " pdb=" C ARG C 66 " ideal model delta sigma weight residual 113.88 101.38 12.50 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG K 66 " pdb=" CA ARG K 66 " pdb=" C ARG K 66 " ideal model delta sigma weight residual 113.88 101.40 12.48 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N HIS E 72 " pdb=" CA HIS E 72 " pdb=" C HIS E 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 angle pdb=" N HIS F 72 " pdb=" CA HIS F 72 " pdb=" C HIS F 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13770 17.99 - 35.98: 378 35.98 - 53.97: 99 53.97 - 71.97: 54 71.97 - 89.96: 21 Dihedral angle restraints: 14322 sinusoidal: 5661 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.36 -40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.35 -40.35 1 1.00e+01 1.00e-02 2.28e+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 93.00 133.34 -40.34 1 1.00e+01 1.00e-02 2.28e+01 ... (remaining 14319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3436 0.115 - 0.229: 1000 0.229 - 0.344: 127 0.344 - 0.459: 18 0.459 - 0.573: 21 Chirality restraints: 4602 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 4599 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.42e+01 pdb=" C7 NAG Z 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.41e+01 pdb=" C7 NAG t 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG t 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG t 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG t 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.063 2.00e-02 2.50e+03 5.21e-02 3.40e+01 pdb=" C7 NAG j 1 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8160 2.82 - 3.34: 23259 3.34 - 3.86: 43967 3.86 - 4.38: 51813 4.38 - 4.90: 83268 Nonbonded interactions: 210467 Sorted by model distance: nonbonded pdb=" O4 NAG A 659 " pdb=" O6 NAG A 659 " model vdw 2.303 3.040 nonbonded pdb=" O4 NAG E 659 " pdb=" O6 NAG E 659 " model vdw 2.304 3.040 nonbonded pdb=" O4 NAG F 659 " pdb=" O6 NAG F 659 " model vdw 2.304 3.040 nonbonded pdb=" O LEU G 568 " pdb=" OG1 THR G 569 " model vdw 2.340 3.040 nonbonded pdb=" O LEU I 568 " pdb=" OG1 THR I 569 " model vdw 2.341 3.040 ... (remaining 210462 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'd' selection = chain 'f' selection = chain 'n' selection = chain 'p' } ncs_group { reference = (chain 'U' and (resid 2 or resid 5 through 9)) selection = (chain 'W' and (resid 1 or resid 4 through 8)) selection = (chain 'Y' and (resid 2 or resid 5 through 9)) selection = (chain 'e' and (resid 2 or resid 5 through 9)) selection = (chain 'g' and (resid 1 or resid 4 through 8)) selection = (chain 'i' and (resid 2 or resid 5 through 9)) selection = (chain 'o' and (resid 2 or resid 5 through 9)) selection = (chain 'q' and (resid 1 or resid 4 through 8)) selection = (chain 's' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 't' selection = chain 'u' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.760 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.023 0.212 26541 Z= 1.203 Angle : 1.869 12.505 36354 Z= 1.152 Chirality : 0.110 0.573 4602 Planarity : 0.009 0.052 4233 Dihedral : 10.403 89.958 8634 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.13 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.38 (0.15), residues: 2967 helix: -1.25 (0.22), residues: 393 sheet: 0.81 (0.14), residues: 1107 loop : 0.41 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 38 TYR 0.077 0.010 TYR K 91 PHE 0.047 0.007 PHE D 71 TRP 0.061 0.009 TRP D 35 HIS 0.011 0.003 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02283 / 1.20 (26313) covalent geometry : angle 1.84033 / 1.15 (35712) SS BOND : bond 0.02554 / 1.20 ( 42) SS BOND : angle 3.00778 / 2.09 ( 84) hydrogen bonds : bond 0.16104 / 10.64 ( 909) hydrogen bonds : angle 7.86563 / 5.47 ( 2421) link_ALPHA1-2 : bond 0.03788 / 2.43 ( 24) link_ALPHA1-2 : angle 2.38211 / 1.60 ( 72) link_ALPHA1-3 : bond 0.03730 / 2.34 ( 30) link_ALPHA1-3 : angle 3.60087 / 2.37 ( 90) link_ALPHA1-6 : bond 0.03088 / 1.95 ( 30) link_ALPHA1-6 : angle 2.89907 / 1.96 ( 90) link_BETA1-4 : bond 0.03015 / 1.97 ( 51) link_BETA1-4 : angle 3.11162 / 2.14 ( 153) link_NAG-ASN : bond 0.03377 / 2.09 ( 51) link_NAG-ASN : angle 3.13175 / 2.13 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9309 (tpp) cc_final: 0.8883 (tpt) REVERT: A 377 ASN cc_start: 0.8428 (t0) cc_final: 0.7977 (p0) REVERT: A 491 ILE cc_start: 0.8624 (mp) cc_final: 0.8389 (tp) REVERT: B 535 MET cc_start: 0.8445 (mtt) cc_final: 0.7983 (tpt) REVERT: L 42 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8187 (pttt) REVERT: L 55 LYS cc_start: 0.8089 (tttm) cc_final: 0.7764 (tttt) REVERT: L 79 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7235 (tm-30) REVERT: H 2 VAL cc_start: 0.7847 (t) cc_final: 0.7575 (p) REVERT: H 26 ASN cc_start: 0.8214 (m-40) cc_final: 0.7699 (m-40) REVERT: D 33 LEU cc_start: 0.6981 (tt) cc_final: 0.6481 (tt) REVERT: D 61 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8123 (mtm-85) REVERT: D 82 ASP cc_start: 0.8349 (m-30) cc_final: 0.7226 (m-30) REVERT: C 26 ASN cc_start: 0.8534 (m-40) cc_final: 0.8050 (m-40) REVERT: C 29 ILE cc_start: 0.8544 (pt) cc_final: 0.7914 (mm) REVERT: C 34 MET cc_start: 0.8751 (mmm) cc_final: 0.8321 (mmm) REVERT: C 76 ASP cc_start: 0.8127 (m-30) cc_final: 0.7670 (m-30) REVERT: E 377 ASN cc_start: 0.8469 (t0) cc_final: 0.8086 (p0) REVERT: G 601 LYS cc_start: 0.8702 (pttm) cc_final: 0.8297 (pttm) REVERT: Q 42 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8370 (pttt) REVERT: Q 79 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7033 (tm-30) REVERT: O 26 ASN cc_start: 0.8248 (m-40) cc_final: 0.8004 (m-40) REVERT: M 33 LEU cc_start: 0.7093 (tt) cc_final: 0.6674 (tt) REVERT: M 61 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: M 82 ASP cc_start: 0.8624 (m-30) cc_final: 0.7530 (m-30) REVERT: J 26 ASN cc_start: 0.7912 (m-40) cc_final: 0.7528 (m-40) REVERT: J 34 MET cc_start: 0.8666 (mmm) cc_final: 0.8356 (mmm) REVERT: J 72 ASP cc_start: 0.6786 (t0) cc_final: 0.5420 (t70) REVERT: F 122 LEU cc_start: 0.9254 (mt) cc_final: 0.9041 (mm) REVERT: F 125 LEU cc_start: 0.9153 (mp) cc_final: 0.8940 (tp) REVERT: F 161 MET cc_start: 0.9213 (tpp) cc_final: 0.8485 (tpt) REVERT: R 42 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7978 (pttt) REVERT: R 78 LEU cc_start: 0.8553 (tp) cc_final: 0.8332 (tp) REVERT: R 79 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6917 (tm-30) REVERT: P 26 ASN cc_start: 0.8142 (m-40) cc_final: 0.7795 (m-40) REVERT: N 61 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7779 (mtm-85) REVERT: N 80 PHE cc_start: 0.8796 (m-80) cc_final: 0.8580 (m-80) REVERT: N 82 ASP cc_start: 0.8536 (m-30) cc_final: 0.7432 (m-30) REVERT: N 91 TYR cc_start: 0.4513 (p90) cc_final: 0.4099 (p90) REVERT: N 100 GLN cc_start: 0.9065 (pm20) cc_final: 0.8770 (pm20) REVERT: K 26 ASN cc_start: 0.7822 (m-40) cc_final: 0.7455 (m-40) REVERT: K 29 ILE cc_start: 0.8614 (pt) cc_final: 0.8133 (mm) REVERT: K 34 MET cc_start: 0.8601 (mmm) cc_final: 0.8142 (mmm) REVERT: K 72 ASP cc_start: 0.7018 (t0) cc_final: 0.4943 (t0) REVERT: K 76 ASP cc_start: 0.8219 (m-30) cc_final: 0.7714 (m-30) outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.2069 time to fit residues: 225.5302 Evaluate side-chains 336 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 590 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 656 ASN ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 195 ASN F 328 GLN I 575 GLN I 616 ASN ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.087946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062930 restraints weight = 89547.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065441 restraints weight = 43424.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067100 restraints weight = 28644.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068148 restraints weight = 22305.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068771 restraints weight = 19155.136| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26541 Z= 0.202 Angle : 0.838 8.765 36354 Z= 0.427 Chirality : 0.048 0.206 4602 Planarity : 0.005 0.089 4233 Dihedral : 5.575 34.442 3243 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.72 % Favored : 94.98 % Rotamer: Outliers : 2.53 % Allowed : 9.22 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.23 (0.15), residues: 2967 helix: 0.10 (0.27), residues: 372 sheet: 0.58 (0.15), residues: 1062 loop : -0.03 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 61 TYR 0.026 0.002 TYR Q 49 PHE 0.024 0.003 PHE D 71 TRP 0.023 0.002 TRP I 631 HIS 0.007 0.001 HIS Q 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (26313) covalent geometry : angle 0.80942 / 0.42 (35712) SS BOND : bond 0.00448 / 0.34 ( 42) SS BOND : angle 1.27955 / 0.84 ( 84) hydrogen bonds : bond 0.05663 / 3.76 ( 909) hydrogen bonds : angle 6.61139 / 4.59 ( 2421) link_ALPHA1-2 : bond 0.00401 / 0.26 ( 24) link_ALPHA1-2 : angle 1.75871 / 1.24 ( 72) link_ALPHA1-3 : bond 0.00653 / 0.42 ( 30) link_ALPHA1-3 : angle 1.80073 / 1.23 ( 90) link_ALPHA1-6 : bond 0.00914 / 0.59 ( 30) link_ALPHA1-6 : angle 1.75352 / 1.19 ( 90) link_BETA1-4 : bond 0.00515 / 0.34 ( 51) link_BETA1-4 : angle 1.92315 / 1.29 ( 153) link_NAG-ASN : bond 0.00399 / 0.25 ( 51) link_NAG-ASN : angle 2.05024 / 1.36 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8011 (mtm) cc_final: 0.7786 (mtm) REVERT: A 271 MET cc_start: 0.7850 (mmm) cc_final: 0.7483 (mmm) REVERT: B 535 MET cc_start: 0.8402 (mtt) cc_final: 0.8187 (tpt) REVERT: B 543 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7266 (t0) REVERT: B 584 GLU cc_start: 0.8682 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 625 ASN cc_start: 0.8787 (m110) cc_final: 0.8329 (m-40) REVERT: B 641 ILE cc_start: 0.9067 (mp) cc_final: 0.8856 (pt) REVERT: B 651 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7861 (p0) REVERT: B 659 ASP cc_start: 0.8075 (m-30) cc_final: 0.7786 (t70) REVERT: L 4 MET cc_start: 0.7052 (ttp) cc_final: 0.6841 (ttt) REVERT: L 42 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8394 (mmmt) REVERT: L 79 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7512 (tm-30) REVERT: H 79 TYR cc_start: 0.7881 (m-80) cc_final: 0.7321 (m-10) REVERT: D 33 LEU cc_start: 0.6110 (tt) cc_final: 0.5791 (tt) REVERT: C 34 MET cc_start: 0.8611 (mmm) cc_final: 0.8192 (mmm) REVERT: C 75 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7305 (mm-30) REVERT: E 137 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7226 (p0) REVERT: E 434 MET cc_start: 0.8587 (ttp) cc_final: 0.8041 (ttp) REVERT: G 535 MET cc_start: 0.7567 (tpt) cc_final: 0.6898 (tpp) REVERT: G 542 ARG cc_start: 0.7665 (ttt-90) cc_final: 0.7103 (mtt-85) REVERT: G 625 ASN cc_start: 0.9096 (m-40) cc_final: 0.8653 (m-40) REVERT: G 651 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7567 (p0) REVERT: Q 79 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7200 (tm-30) REVERT: O 26 ASN cc_start: 0.7932 (m-40) cc_final: 0.7602 (m110) REVERT: O 72 ASP cc_start: 0.7841 (t0) cc_final: 0.7523 (m-30) REVERT: O 79 TYR cc_start: 0.7859 (m-80) cc_final: 0.7642 (m-10) REVERT: O 82 MET cc_start: 0.7460 (mtp) cc_final: 0.6739 (ttm) REVERT: J 19 ILE cc_start: 0.8531 (mm) cc_final: 0.8323 (mm) REVERT: J 100 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6431 (m-30) REVERT: F 104 MET cc_start: 0.8543 (tpp) cc_final: 0.7997 (tpp) REVERT: F 161 MET cc_start: 0.8816 (tpp) cc_final: 0.8549 (tpt) REVERT: I 535 MET cc_start: 0.8217 (tpt) cc_final: 0.7850 (mmm) REVERT: I 584 GLU cc_start: 0.8455 (tt0) cc_final: 0.8107 (tm-30) REVERT: I 641 ILE cc_start: 0.8965 (mp) cc_final: 0.8757 (pt) REVERT: I 649 SER cc_start: 0.8964 (m) cc_final: 0.8476 (p) REVERT: R 4 MET cc_start: 0.7439 (ttp) cc_final: 0.7234 (ttp) REVERT: R 78 LEU cc_start: 0.8803 (tp) cc_final: 0.8297 (pp) REVERT: R 79 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7145 (tm-30) REVERT: P 26 ASN cc_start: 0.7822 (m-40) cc_final: 0.7610 (m-40) REVERT: P 72 ASP cc_start: 0.7703 (t0) cc_final: 0.7405 (m-30) REVERT: P 79 TYR cc_start: 0.7654 (m-80) cc_final: 0.7361 (m-10) REVERT: P 99 ARG cc_start: 0.8178 (tpm170) cc_final: 0.7936 (tpm170) REVERT: N 23 CYS cc_start: 0.2179 (p) cc_final: 0.0106 (p) REVERT: N 91 TYR cc_start: 0.4878 (p90) cc_final: 0.4355 (p90) REVERT: K 34 MET cc_start: 0.8499 (mmm) cc_final: 0.7726 (mmm) REVERT: K 82 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9191 (mtmm) outliers start: 66 outliers final: 31 residues processed: 460 average time/residue: 0.1852 time to fit residues: 132.6492 Evaluate side-chains 340 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 127 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 209 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 267 optimal weight: 0.0370 chunk 88 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN O 81 GLN M 79 GLN J 26 ASN J 82AHIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN F 377 ASN I 653 GLN P 81 GLN N 79 GLN K 26 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062452 restraints weight = 90097.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064969 restraints weight = 43680.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066656 restraints weight = 28858.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067713 restraints weight = 22463.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068243 restraints weight = 19326.539| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26541 Z= 0.155 Angle : 0.732 9.437 36354 Z= 0.366 Chirality : 0.044 0.205 4602 Planarity : 0.004 0.066 4233 Dihedral : 5.391 29.501 3243 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 2.34 % Allowed : 10.83 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.10 (0.15), residues: 2967 helix: 0.57 (0.28), residues: 354 sheet: 0.58 (0.16), residues: 978 loop : -0.31 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 39 TYR 0.020 0.002 TYR Q 49 PHE 0.024 0.002 PHE M 98 TRP 0.018 0.001 TRP F 112 HIS 0.014 0.001 HIS J 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (26313) covalent geometry : angle 0.70898 / 0.36 (35712) SS BOND : bond 0.00278 / 0.19 ( 42) SS BOND : angle 0.97168 / 0.61 ( 84) hydrogen bonds : bond 0.04607 / 3.08 ( 909) hydrogen bonds : angle 6.19781 / 4.32 ( 2421) link_ALPHA1-2 : bond 0.00384 / 0.24 ( 24) link_ALPHA1-2 : angle 1.67649 / 1.17 ( 72) link_ALPHA1-3 : bond 0.00608 / 0.39 ( 30) link_ALPHA1-3 : angle 1.58765 / 1.07 ( 90) link_ALPHA1-6 : bond 0.00876 / 0.54 ( 30) link_ALPHA1-6 : angle 1.63264 / 1.09 ( 90) link_BETA1-4 : bond 0.00412 / 0.27 ( 51) link_BETA1-4 : angle 1.50266 / 1.01 ( 153) link_NAG-ASN : bond 0.00266 / 0.17 ( 51) link_NAG-ASN : angle 1.73435 / 1.14 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 343 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8891 (tpp) cc_final: 0.8326 (tpp) REVERT: A 217 TYR cc_start: 0.8519 (m-80) cc_final: 0.7996 (m-80) REVERT: B 584 GLU cc_start: 0.8684 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 651 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 659 ASP cc_start: 0.7811 (m-30) cc_final: 0.7353 (t0) REVERT: L 4 MET cc_start: 0.7282 (ttp) cc_final: 0.7071 (ttt) REVERT: L 42 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8445 (mmmt) REVERT: L 79 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7513 (tm-30) REVERT: H 68 THR cc_start: 0.8869 (m) cc_final: 0.8506 (t) REVERT: H 72 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: H 79 TYR cc_start: 0.7741 (m-80) cc_final: 0.7321 (m-10) REVERT: H 100 ASN cc_start: 0.7449 (m-40) cc_final: 0.7130 (t0) REVERT: D 54 LEU cc_start: 0.8712 (pp) cc_final: 0.8434 (tt) REVERT: C 26 ASN cc_start: 0.8204 (m110) cc_final: 0.7930 (m110) REVERT: C 34 MET cc_start: 0.8381 (mmm) cc_final: 0.8059 (mmm) REVERT: E 137 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.6974 (p0) REVERT: E 434 MET cc_start: 0.8527 (ttp) cc_final: 0.7943 (ttp) REVERT: G 535 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7661 (mmm) REVERT: G 542 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.7126 (mtt-85) REVERT: G 595 ILE cc_start: 0.8183 (mt) cc_final: 0.7976 (mm) REVERT: G 601 LYS cc_start: 0.9082 (pttm) cc_final: 0.8516 (ptpt) REVERT: G 625 ASN cc_start: 0.9037 (m-40) cc_final: 0.8568 (t0) REVERT: Q 4 MET cc_start: 0.7618 (ttp) cc_final: 0.7378 (ttt) REVERT: Q 42 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8127 (mmmm) REVERT: Q 48 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7354 (mm) REVERT: Q 79 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7077 (tm-30) REVERT: O 26 ASN cc_start: 0.8078 (m-40) cc_final: 0.7821 (m110) REVERT: O 72 ASP cc_start: 0.7797 (t0) cc_final: 0.7506 (m-30) REVERT: O 79 TYR cc_start: 0.8037 (m-80) cc_final: 0.7310 (m-10) REVERT: J 100 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6343 (m-30) REVERT: F 161 MET cc_start: 0.8620 (tpp) cc_final: 0.8362 (tpt) REVERT: I 530 MET cc_start: 0.7735 (mmt) cc_final: 0.7439 (mmt) REVERT: I 535 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7536 (mmm) REVERT: I 584 GLU cc_start: 0.8423 (tt0) cc_final: 0.8096 (tm-30) REVERT: I 641 ILE cc_start: 0.8944 (mp) cc_final: 0.8732 (pt) REVERT: I 648 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8588 (pp20) REVERT: R 42 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8519 (mmtp) REVERT: R 78 LEU cc_start: 0.8741 (tp) cc_final: 0.8313 (pp) REVERT: R 79 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6901 (tm-30) REVERT: P 26 ASN cc_start: 0.7775 (m-40) cc_final: 0.7548 (m-40) REVERT: P 68 THR cc_start: 0.9022 (m) cc_final: 0.8691 (t) REVERT: P 72 ASP cc_start: 0.7597 (t0) cc_final: 0.7286 (m-30) REVERT: P 79 TYR cc_start: 0.8017 (m-80) cc_final: 0.7344 (m-10) REVERT: N 54 LEU cc_start: 0.8666 (pp) cc_final: 0.8409 (tt) REVERT: K 26 ASN cc_start: 0.7553 (m-40) cc_final: 0.7339 (m110) REVERT: K 34 MET cc_start: 0.8532 (mmm) cc_final: 0.8229 (mmm) outliers start: 61 outliers final: 27 residues processed: 383 average time/residue: 0.1844 time to fit residues: 111.3499 Evaluate side-chains 321 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain Q residue 24 ARG Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 241 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 chunk 229 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 195 ASN B 543 ASN L 100 GLN H 81 GLN D 89 GLN E 170 GLN E 195 ASN E 328 GLN Q 100 GLN O 82AHIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 170 GLN F 195 ASN I 652 GLN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN N 89 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.083712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058407 restraints weight = 90386.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060797 restraints weight = 44402.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062340 restraints weight = 29694.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063319 restraints weight = 23493.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063886 restraints weight = 20374.213| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26541 Z= 0.255 Angle : 0.801 10.282 36354 Z= 0.393 Chirality : 0.046 0.230 4602 Planarity : 0.005 0.065 4233 Dihedral : 5.449 32.469 3243 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 3.73 % Allowed : 11.25 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.10 (0.15), residues: 2967 helix: 0.35 (0.28), residues: 351 sheet: 0.38 (0.17), residues: 936 loop : -0.36 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 83 TYR 0.020 0.002 TYR R 49 PHE 0.020 0.003 PHE D 71 TRP 0.022 0.002 TRP F 112 HIS 0.024 0.002 HIS J 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.26 (26313) covalent geometry : angle 0.77182 / 0.39 (35712) SS BOND : bond 0.00449 / 0.32 ( 42) SS BOND : angle 1.19670 / 0.77 ( 84) hydrogen bonds : bond 0.04601 / 3.09 ( 909) hydrogen bonds : angle 6.16214 / 4.30 ( 2421) link_ALPHA1-2 : bond 0.00259 / 0.16 ( 24) link_ALPHA1-2 : angle 2.25653 / 1.58 ( 72) link_ALPHA1-3 : bond 0.00493 / 0.33 ( 30) link_ALPHA1-3 : angle 1.67940 / 1.14 ( 90) link_ALPHA1-6 : bond 0.00678 / 0.43 ( 30) link_ALPHA1-6 : angle 1.76278 / 1.19 ( 90) link_BETA1-4 : bond 0.00430 / 0.27 ( 51) link_BETA1-4 : angle 1.70545 / 1.14 ( 153) link_NAG-ASN : bond 0.00529 / 0.31 ( 51) link_NAG-ASN : angle 1.93925 / 1.31 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 291 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8963 (tpp) cc_final: 0.8302 (tpp) REVERT: B 543 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7359 (t0) REVERT: B 651 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7956 (p0) REVERT: B 659 ASP cc_start: 0.7654 (m-30) cc_final: 0.7251 (t0) REVERT: L 4 MET cc_start: 0.7700 (ttp) cc_final: 0.7446 (ttp) REVERT: L 42 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8483 (mmmt) REVERT: L 79 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7246 (tm-30) REVERT: H 68 THR cc_start: 0.9115 (m) cc_final: 0.8695 (t) REVERT: H 72 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: H 79 TYR cc_start: 0.7863 (m-80) cc_final: 0.7524 (m-80) REVERT: H 82 MET cc_start: 0.8072 (mtp) cc_final: 0.7788 (ttm) REVERT: H 99 ARG cc_start: 0.7928 (tpm170) cc_final: 0.7698 (tpp-160) REVERT: D 33 LEU cc_start: 0.5933 (tp) cc_final: 0.5588 (tp) REVERT: D 39 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6418 (mmtm) REVERT: D 42 LYS cc_start: 0.8352 (mmtp) cc_final: 0.8080 (pttt) REVERT: D 54 LEU cc_start: 0.8738 (pp) cc_final: 0.8513 (tt) REVERT: D 103 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8196 (mpp-170) REVERT: C 19 ILE cc_start: 0.8463 (mm) cc_final: 0.8250 (mm) REVERT: C 34 MET cc_start: 0.8567 (mmm) cc_final: 0.7993 (mmm) REVERT: C 85 GLU cc_start: 0.9200 (tp30) cc_final: 0.8909 (mp0) REVERT: E 137 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7596 (p0) REVERT: E 423 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8746 (mp) REVERT: E 434 MET cc_start: 0.8602 (ttp) cc_final: 0.8117 (ttp) REVERT: G 530 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: G 535 MET cc_start: 0.7651 (tpt) cc_final: 0.7152 (mmt) REVERT: G 542 ARG cc_start: 0.7730 (ttt-90) cc_final: 0.7195 (mtt-85) REVERT: G 625 ASN cc_start: 0.8768 (m-40) cc_final: 0.8457 (m-40) REVERT: G 626 MET cc_start: 0.7500 (tmm) cc_final: 0.6805 (tmm) REVERT: Q 48 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7350 (mm) REVERT: Q 105 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6439 (pm20) REVERT: O 26 ASN cc_start: 0.8030 (m-40) cc_final: 0.7730 (m110) REVERT: O 68 THR cc_start: 0.9055 (m) cc_final: 0.8668 (p) REVERT: O 79 TYR cc_start: 0.8125 (m-80) cc_final: 0.7850 (m-80) REVERT: O 100 ASN cc_start: 0.8315 (m-40) cc_final: 0.8068 (t0) REVERT: M 82 ASP cc_start: 0.7761 (m-30) cc_final: 0.7535 (m-30) REVERT: M 103 ARG cc_start: 0.8512 (mpp-170) cc_final: 0.7756 (tpp80) REVERT: J 85 GLU cc_start: 0.9228 (tp30) cc_final: 0.8983 (mp0) REVERT: J 100 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: F 195 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7518 (t0) REVERT: F 271 MET cc_start: 0.7915 (mmm) cc_final: 0.7710 (mmm) REVERT: I 535 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7288 (mmm) REVERT: I 584 GLU cc_start: 0.8401 (tt0) cc_final: 0.8101 (tm-30) REVERT: I 647 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7107 (mt-10) REVERT: R 42 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8561 (mmtp) REVERT: R 78 LEU cc_start: 0.8737 (tp) cc_final: 0.8290 (pp) REVERT: R 79 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6852 (tm-30) REVERT: N 54 LEU cc_start: 0.8839 (pp) cc_final: 0.8627 (tt) REVERT: K 19 ILE cc_start: 0.8602 (mm) cc_final: 0.8386 (mm) REVERT: K 34 MET cc_start: 0.8541 (mmm) cc_final: 0.8178 (mmm) REVERT: K 85 GLU cc_start: 0.9210 (tp30) cc_final: 0.8802 (mp0) REVERT: K 100 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7765 (t0) outliers start: 97 outliers final: 58 residues processed: 357 average time/residue: 0.1812 time to fit residues: 102.7601 Evaluate side-chains 331 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 261 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 222 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN E 195 ASN E 328 GLN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN F 195 ASN F 328 GLN I 575 GLN ** I 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN N 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.085336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060184 restraints weight = 90008.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062648 restraints weight = 43844.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064264 restraints weight = 29129.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065266 restraints weight = 22866.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065881 restraints weight = 19783.389| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26541 Z= 0.141 Angle : 0.694 10.761 36354 Z= 0.340 Chirality : 0.044 0.230 4602 Planarity : 0.004 0.086 4233 Dihedral : 5.182 28.809 3243 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.96 % Allowed : 11.98 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.18 (0.15), residues: 2967 helix: 0.44 (0.28), residues: 366 sheet: 0.34 (0.16), residues: 948 loop : -0.47 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 24 TYR 0.018 0.001 TYR R 49 PHE 0.013 0.002 PHE D 71 TRP 0.035 0.001 TRP D 35 HIS 0.007 0.001 HIS J 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (26313) covalent geometry : angle 0.66834 / 0.34 (35712) SS BOND : bond 0.00380 / 0.27 ( 42) SS BOND : angle 1.21850 / 0.73 ( 84) hydrogen bonds : bond 0.04079 / 2.74 ( 909) hydrogen bonds : angle 5.92983 / 4.14 ( 2421) link_ALPHA1-2 : bond 0.00383 / 0.22 ( 24) link_ALPHA1-2 : angle 1.78897 / 1.25 ( 72) link_ALPHA1-3 : bond 0.00527 / 0.34 ( 30) link_ALPHA1-3 : angle 1.61127 / 1.08 ( 90) link_ALPHA1-6 : bond 0.00762 / 0.46 ( 30) link_ALPHA1-6 : angle 1.66680 / 1.11 ( 90) link_BETA1-4 : bond 0.00339 / 0.22 ( 51) link_BETA1-4 : angle 1.39692 / 0.93 ( 153) link_NAG-ASN : bond 0.00270 / 0.17 ( 51) link_NAG-ASN : angle 1.60750 / 1.05 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 298 time to evaluate : 1.051 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 91 GLU cc_start: 0.7567 (tp30) cc_final: 0.7219 (mm-30) REVERT: A 104 MET cc_start: 0.8852 (tpp) cc_final: 0.8141 (tpp) REVERT: A 161 MET cc_start: 0.8979 (tpt) cc_final: 0.8638 (tpt) REVERT: L 4 MET cc_start: 0.7900 (ttp) cc_final: 0.7592 (ttp) REVERT: L 42 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8492 (mmmt) REVERT: L 79 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7414 (tm-30) REVERT: L 86 TYR cc_start: 0.7492 (m-80) cc_final: 0.7284 (m-80) REVERT: H 36 TRP cc_start: 0.8081 (m100) cc_final: 0.7825 (m100) REVERT: H 68 THR cc_start: 0.9118 (m) cc_final: 0.8775 (p) REVERT: H 72 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: H 79 TYR cc_start: 0.7781 (m-80) cc_final: 0.7477 (m-80) REVERT: H 82 MET cc_start: 0.7381 (mmp) cc_final: 0.7065 (mmm) REVERT: D 42 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8046 (mmtm) REVERT: D 103 ARG cc_start: 0.8627 (ptp90) cc_final: 0.8157 (mpp-170) REVERT: C 34 MET cc_start: 0.8510 (mmm) cc_final: 0.7923 (mmm) REVERT: C 85 GLU cc_start: 0.9210 (tp30) cc_final: 0.8843 (mp0) REVERT: C 100 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: E 137 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7522 (p0) REVERT: E 434 MET cc_start: 0.8544 (ttp) cc_final: 0.8102 (ttp) REVERT: G 530 MET cc_start: 0.8486 (mmm) cc_final: 0.8252 (mmm) REVERT: G 535 MET cc_start: 0.7688 (tpt) cc_final: 0.7202 (mmt) REVERT: G 542 ARG cc_start: 0.7720 (ttt-90) cc_final: 0.7181 (mtt-85) REVERT: G 625 ASN cc_start: 0.8791 (m-40) cc_final: 0.8469 (m-40) REVERT: G 626 MET cc_start: 0.7349 (tmm) cc_final: 0.6742 (tmm) REVERT: Q 48 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7493 (mm) REVERT: Q 55 LYS cc_start: 0.7937 (tttp) cc_final: 0.7468 (ttmt) REVERT: Q 105 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6488 (pm20) REVERT: O 26 ASN cc_start: 0.8015 (m-40) cc_final: 0.7719 (m110) REVERT: O 68 THR cc_start: 0.8963 (m) cc_final: 0.8600 (p) REVERT: O 72 ASP cc_start: 0.8033 (t0) cc_final: 0.7167 (m-30) REVERT: O 79 TYR cc_start: 0.8092 (m-80) cc_final: 0.7816 (m-80) REVERT: M 82 ASP cc_start: 0.7725 (m-30) cc_final: 0.7468 (m-30) REVERT: M 103 ARG cc_start: 0.8626 (mpp-170) cc_final: 0.7859 (tpp80) REVERT: J 11 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8148 (tp) REVERT: J 85 GLU cc_start: 0.9269 (tp30) cc_final: 0.8957 (mp0) REVERT: F 271 MET cc_start: 0.7919 (mmm) cc_final: 0.7688 (mmm) REVERT: I 535 MET cc_start: 0.7936 (tpt) cc_final: 0.7605 (mmm) REVERT: I 584 GLU cc_start: 0.8366 (tt0) cc_final: 0.8058 (tm-30) REVERT: I 601 LYS cc_start: 0.9128 (pttm) cc_final: 0.8698 (pttm) REVERT: I 647 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7194 (mt-10) REVERT: R 42 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8532 (mmtp) REVERT: R 78 LEU cc_start: 0.8720 (tp) cc_final: 0.8319 (pp) REVERT: R 79 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6882 (tm-30) REVERT: P 68 THR cc_start: 0.9024 (m) cc_final: 0.8609 (p) REVERT: K 34 MET cc_start: 0.8584 (mmm) cc_final: 0.8142 (mmm) REVERT: K 100 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6668 (t0) REVERT: K 100 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7538 (t0) REVERT: K 110 THR cc_start: 0.8366 (m) cc_final: 0.7875 (p) outliers start: 77 outliers final: 49 residues processed: 347 average time/residue: 0.1794 time to fit residues: 99.1019 Evaluate side-chains 322 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 287 optimal weight: 0.0980 chunk 239 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN D 90 HIS E 130 GLN E 195 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 195 ASN I 575 GLN I 590 GLN R 89 GLN N 37 GLN N 90 HIS K 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.084660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059507 restraints weight = 90646.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061942 restraints weight = 44190.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063547 restraints weight = 29338.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064552 restraints weight = 23017.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065170 restraints weight = 19873.594| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26541 Z= 0.158 Angle : 0.688 8.911 36354 Z= 0.337 Chirality : 0.044 0.224 4602 Planarity : 0.004 0.076 4233 Dihedral : 5.072 28.416 3243 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.61 % Rotamer: Outliers : 3.53 % Allowed : 12.33 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.05 (0.15), residues: 2967 helix: 0.56 (0.28), residues: 363 sheet: 0.47 (0.17), residues: 942 loop : -0.42 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 38 TYR 0.018 0.001 TYR R 49 PHE 0.012 0.002 PHE A 53 TRP 0.023 0.002 TRP N 35 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (26313) covalent geometry : angle 0.66301 / 0.33 (35712) SS BOND : bond 0.00450 / 0.27 ( 42) SS BOND : angle 0.86140 / 0.57 ( 84) hydrogen bonds : bond 0.03992 / 2.69 ( 909) hydrogen bonds : angle 5.86057 / 4.11 ( 2421) link_ALPHA1-2 : bond 0.00280 / 0.16 ( 24) link_ALPHA1-2 : angle 1.90014 / 1.32 ( 72) link_ALPHA1-3 : bond 0.00518 / 0.34 ( 30) link_ALPHA1-3 : angle 1.59883 / 1.07 ( 90) link_ALPHA1-6 : bond 0.00715 / 0.43 ( 30) link_ALPHA1-6 : angle 1.68394 / 1.12 ( 90) link_BETA1-4 : bond 0.00320 / 0.21 ( 51) link_BETA1-4 : angle 1.43162 / 0.96 ( 153) link_NAG-ASN : bond 0.00313 / 0.19 ( 51) link_NAG-ASN : angle 1.59047 / 1.06 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 306 time to evaluate : 0.938 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: A 104 MET cc_start: 0.8868 (tpp) cc_final: 0.8157 (tpp) REVERT: B 530 MET cc_start: 0.7864 (mtm) cc_final: 0.7651 (mtp) REVERT: B 651 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7894 (p0) REVERT: L 4 MET cc_start: 0.7866 (ttp) cc_final: 0.7638 (ttp) REVERT: L 79 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7409 (tm-30) REVERT: L 86 TYR cc_start: 0.7810 (m-80) cc_final: 0.7571 (m-80) REVERT: H 68 THR cc_start: 0.9063 (m) cc_final: 0.8709 (p) REVERT: H 72 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: H 82 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8525 (mtmm) REVERT: H 99 ARG cc_start: 0.8003 (tpm170) cc_final: 0.7709 (mmm160) REVERT: D 39 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6255 (mmtm) REVERT: D 42 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8202 (pttt) REVERT: D 48 ILE cc_start: 0.7295 (mp) cc_final: 0.6896 (mt) REVERT: D 82 ASP cc_start: 0.7508 (m-30) cc_final: 0.7091 (m-30) REVERT: D 103 ARG cc_start: 0.8741 (ptp90) cc_final: 0.8260 (mpp-170) REVERT: C 11 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8132 (tp) REVERT: C 34 MET cc_start: 0.8540 (mmm) cc_final: 0.7965 (mmm) REVERT: C 85 GLU cc_start: 0.9213 (tp30) cc_final: 0.8852 (mp0) REVERT: E 423 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8717 (mp) REVERT: E 434 MET cc_start: 0.8564 (ttp) cc_final: 0.8075 (ttp) REVERT: G 530 MET cc_start: 0.8351 (mmm) cc_final: 0.8041 (mmm) REVERT: G 535 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: G 542 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7209 (mtt-85) REVERT: G 625 ASN cc_start: 0.8811 (m-40) cc_final: 0.8434 (m-40) REVERT: G 626 MET cc_start: 0.7447 (tmm) cc_final: 0.6803 (tmm) REVERT: Q 48 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7421 (mm) REVERT: O 26 ASN cc_start: 0.7871 (m-40) cc_final: 0.7580 (m110) REVERT: O 68 THR cc_start: 0.8925 (m) cc_final: 0.8570 (p) REVERT: O 72 ASP cc_start: 0.8060 (t0) cc_final: 0.7344 (m-30) REVERT: O 75 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8296 (mp0) REVERT: O 79 TYR cc_start: 0.8095 (m-80) cc_final: 0.7770 (m-10) REVERT: M 39 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7314 (mmtm) REVERT: M 42 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8374 (pttt) REVERT: M 103 ARG cc_start: 0.8755 (mpp-170) cc_final: 0.8060 (tpp80) REVERT: J 11 LEU cc_start: 0.8613 (mp) cc_final: 0.8307 (tp) REVERT: J 85 GLU cc_start: 0.9184 (tp30) cc_final: 0.8875 (mp0) REVERT: J 100 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.6079 (t0) REVERT: F 271 MET cc_start: 0.8015 (mmm) cc_final: 0.7652 (mmm) REVERT: I 535 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7296 (mmm) REVERT: I 584 GLU cc_start: 0.8377 (tt0) cc_final: 0.8077 (tm-30) REVERT: I 601 LYS cc_start: 0.9172 (pttm) cc_final: 0.8598 (pttm) REVERT: I 625 ASN cc_start: 0.8988 (m-40) cc_final: 0.8547 (t0) REVERT: I 652 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: R 78 LEU cc_start: 0.8745 (tp) cc_final: 0.8307 (pp) REVERT: R 79 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6863 (tm-30) REVERT: N 70 GLU cc_start: 0.9442 (pp20) cc_final: 0.8825 (pm20) REVERT: K 34 MET cc_start: 0.8587 (mmm) cc_final: 0.8033 (mmm) REVERT: K 85 GLU cc_start: 0.9146 (tp30) cc_final: 0.8722 (mp0) REVERT: K 100 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7757 (t0) REVERT: K 110 THR cc_start: 0.8402 (m) cc_final: 0.7904 (p) outliers start: 92 outliers final: 59 residues processed: 361 average time/residue: 0.1857 time to fit residues: 105.1589 Evaluate side-chains 349 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 257 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN E 195 ASN E 328 GLN M 37 GLN ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN I 575 GLN N 90 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058557 restraints weight = 88961.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060908 restraints weight = 43477.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062462 restraints weight = 28875.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063419 restraints weight = 22640.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064028 restraints weight = 19577.936| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26541 Z= 0.202 Angle : 0.725 9.923 36354 Z= 0.352 Chirality : 0.045 0.177 4602 Planarity : 0.005 0.078 4233 Dihedral : 5.096 29.184 3243 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.12 % Favored : 94.78 % Rotamer: Outliers : 3.53 % Allowed : 13.10 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.11 (0.15), residues: 2967 helix: 0.47 (0.28), residues: 366 sheet: 0.43 (0.17), residues: 936 loop : -0.44 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 61 TYR 0.016 0.001 TYR Q 49 PHE 0.014 0.002 PHE A 53 TRP 0.024 0.002 TRP H 36 HIS 0.024 0.001 HIS N 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (26313) covalent geometry : angle 0.69888 / 0.35 (35712) SS BOND : bond 0.00368 / 0.25 ( 42) SS BOND : angle 0.94918 / 0.63 ( 84) hydrogen bonds : bond 0.04029 / 2.70 ( 909) hydrogen bonds : angle 5.81784 / 4.07 ( 2421) link_ALPHA1-2 : bond 0.00221 / 0.13 ( 24) link_ALPHA1-2 : angle 2.05443 / 1.42 ( 72) link_ALPHA1-3 : bond 0.00481 / 0.31 ( 30) link_ALPHA1-3 : angle 1.62367 / 1.09 ( 90) link_ALPHA1-6 : bond 0.00670 / 0.41 ( 30) link_ALPHA1-6 : angle 1.70796 / 1.15 ( 90) link_BETA1-4 : bond 0.00325 / 0.21 ( 51) link_BETA1-4 : angle 1.47590 / 0.99 ( 153) link_NAG-ASN : bond 0.00410 / 0.24 ( 51) link_NAG-ASN : angle 1.69532 / 1.13 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 288 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8888 (tpp) cc_final: 0.8196 (tpp) REVERT: B 584 GLU cc_start: 0.8669 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 651 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7898 (p0) REVERT: L 4 MET cc_start: 0.7894 (ttp) cc_final: 0.7521 (ttp) REVERT: L 79 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7409 (tm-30) REVERT: H 68 THR cc_start: 0.9067 (m) cc_final: 0.8716 (p) REVERT: H 72 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: H 82 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8731 (mtmm) REVERT: D 24 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7361 (mtm-85) REVERT: D 39 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7352 (mmtm) REVERT: D 82 ASP cc_start: 0.7583 (m-30) cc_final: 0.7120 (m-30) REVERT: D 103 ARG cc_start: 0.8785 (ptp90) cc_final: 0.8309 (mpp-170) REVERT: C 11 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8229 (tp) REVERT: C 34 MET cc_start: 0.8547 (mmm) cc_final: 0.7939 (mmm) REVERT: C 82 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8814 (pttm) REVERT: C 85 GLU cc_start: 0.9202 (tp30) cc_final: 0.8850 (mp0) REVERT: C 110 THR cc_start: 0.8423 (m) cc_final: 0.7822 (p) REVERT: E 434 MET cc_start: 0.8598 (ttp) cc_final: 0.8063 (ttp) REVERT: G 535 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7155 (mmt) REVERT: G 625 ASN cc_start: 0.8786 (m-40) cc_final: 0.8388 (m-40) REVERT: G 626 MET cc_start: 0.7551 (tmm) cc_final: 0.7039 (tmm) REVERT: Q 4 MET cc_start: 0.8050 (ttp) cc_final: 0.7717 (tmm) REVERT: Q 48 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7568 (mm) REVERT: O 26 ASN cc_start: 0.7897 (m-40) cc_final: 0.7600 (m110) REVERT: O 68 THR cc_start: 0.8974 (m) cc_final: 0.8597 (p) REVERT: O 72 ASP cc_start: 0.8089 (t0) cc_final: 0.7608 (m-30) REVERT: O 75 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8520 (mm-30) REVERT: M 4 MET cc_start: 0.3455 (ttp) cc_final: 0.3082 (ppp) REVERT: M 39 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7515 (mmtm) REVERT: M 103 ARG cc_start: 0.8804 (mpp-170) cc_final: 0.8073 (tpp80) REVERT: J 11 LEU cc_start: 0.8647 (mp) cc_final: 0.8355 (tp) REVERT: J 85 GLU cc_start: 0.9156 (tp30) cc_final: 0.8826 (mp0) REVERT: J 100 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.6253 (t0) REVERT: F 271 MET cc_start: 0.8109 (mmm) cc_final: 0.7654 (mmm) REVERT: I 535 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7739 (mmt) REVERT: I 584 GLU cc_start: 0.8380 (tt0) cc_final: 0.8137 (tm-30) REVERT: I 601 LYS cc_start: 0.9268 (pttm) cc_final: 0.8752 (pttt) REVERT: I 625 ASN cc_start: 0.9001 (m-40) cc_final: 0.8651 (t0) REVERT: I 651 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7804 (p0) REVERT: R 78 LEU cc_start: 0.8737 (tp) cc_final: 0.8490 (tp) REVERT: R 105 GLU cc_start: 0.7331 (pp20) cc_final: 0.6880 (tm-30) REVERT: P 82 MET cc_start: 0.7789 (tpp) cc_final: 0.7348 (tpp) REVERT: N 42 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8419 (mmmm) REVERT: N 70 GLU cc_start: 0.9432 (pp20) cc_final: 0.8851 (pm20) REVERT: K 34 MET cc_start: 0.8558 (mmm) cc_final: 0.8136 (mmm) REVERT: K 85 GLU cc_start: 0.9194 (tp30) cc_final: 0.8817 (mp0) REVERT: K 100 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7984 (t0) REVERT: K 110 THR cc_start: 0.8515 (m) cc_final: 0.8018 (p) outliers start: 92 outliers final: 64 residues processed: 354 average time/residue: 0.1811 time to fit residues: 101.5351 Evaluate side-chains 344 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 268 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 276 optimal weight: 40.0000 chunk 151 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 189 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 177 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN O 81 GLN ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN I 652 GLN ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN K 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056645 restraints weight = 91887.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058887 restraints weight = 46656.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060358 restraints weight = 31779.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061270 restraints weight = 25360.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061856 restraints weight = 22171.452| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26541 Z= 0.278 Angle : 0.813 11.498 36354 Z= 0.394 Chirality : 0.047 0.201 4602 Planarity : 0.005 0.076 4233 Dihedral : 5.381 33.271 3243 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.17 % Rotamer: Outliers : 3.57 % Allowed : 13.67 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.41 (0.15), residues: 2967 helix: 0.18 (0.27), residues: 369 sheet: 0.17 (0.17), residues: 972 loop : -0.61 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 327 TYR 0.018 0.002 TYR L 91 PHE 0.021 0.002 PHE E 376 TRP 0.022 0.002 TRP H 36 HIS 0.010 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (26313) covalent geometry : angle 0.78238 / 0.39 (35712) SS BOND : bond 0.00492 / 0.34 ( 42) SS BOND : angle 1.19810 / 0.81 ( 84) hydrogen bonds : bond 0.04405 / 2.97 ( 909) hydrogen bonds : angle 5.99181 / 4.18 ( 2421) link_ALPHA1-2 : bond 0.00277 / 0.17 ( 24) link_ALPHA1-2 : angle 2.49345 / 1.72 ( 72) link_ALPHA1-3 : bond 0.00457 / 0.30 ( 30) link_ALPHA1-3 : angle 1.69657 / 1.15 ( 90) link_ALPHA1-6 : bond 0.00629 / 0.38 ( 30) link_ALPHA1-6 : angle 1.78998 / 1.22 ( 90) link_BETA1-4 : bond 0.00372 / 0.23 ( 51) link_BETA1-4 : angle 1.64427 / 1.09 ( 153) link_NAG-ASN : bond 0.00635 / 0.38 ( 51) link_NAG-ASN : angle 2.01882 / 1.39 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 281 time to evaluate : 0.824 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 104 MET cc_start: 0.8928 (tpp) cc_final: 0.8244 (tpp) REVERT: B 584 GLU cc_start: 0.8674 (tt0) cc_final: 0.8287 (tm-30) REVERT: B 651 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7956 (p0) REVERT: L 79 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7418 (tm-30) REVERT: H 68 THR cc_start: 0.9057 (m) cc_final: 0.8707 (p) REVERT: H 72 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: H 79 TYR cc_start: 0.7893 (m-80) cc_final: 0.7503 (m-10) REVERT: D 39 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6553 (mmtm) REVERT: D 42 LYS cc_start: 0.8441 (mmtp) cc_final: 0.8189 (pttt) REVERT: D 103 ARG cc_start: 0.8822 (ptp90) cc_final: 0.8364 (mpp-170) REVERT: C 11 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8335 (tp) REVERT: C 34 MET cc_start: 0.8538 (mmm) cc_final: 0.7961 (mmm) REVERT: C 85 GLU cc_start: 0.9241 (tp30) cc_final: 0.8833 (mp0) REVERT: C 110 THR cc_start: 0.8332 (m) cc_final: 0.7779 (p) REVERT: E 434 MET cc_start: 0.8675 (ttp) cc_final: 0.8117 (ttp) REVERT: G 530 MET cc_start: 0.7820 (mmm) cc_final: 0.7426 (mmm) REVERT: G 535 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7179 (mmt) REVERT: G 625 ASN cc_start: 0.8900 (m-40) cc_final: 0.8561 (m110) REVERT: Q 4 MET cc_start: 0.8195 (ttp) cc_final: 0.7877 (tmm) REVERT: O 68 THR cc_start: 0.9031 (m) cc_final: 0.8660 (p) REVERT: O 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7537 (m-30) REVERT: O 99 ARG cc_start: 0.8238 (tpm170) cc_final: 0.8031 (mmm160) REVERT: M 35 TRP cc_start: 0.6166 (m-10) cc_final: 0.5715 (m-10) REVERT: M 39 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7256 (mmtm) REVERT: M 42 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8360 (mmmm) REVERT: M 103 ARG cc_start: 0.8811 (mpp-170) cc_final: 0.8608 (mpp-170) REVERT: J 11 LEU cc_start: 0.8675 (mp) cc_final: 0.8384 (tp) REVERT: J 85 GLU cc_start: 0.9172 (tp30) cc_final: 0.8868 (mp0) REVERT: J 100 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.6303 (t0) REVERT: F 271 MET cc_start: 0.8201 (mmm) cc_final: 0.7630 (mmm) REVERT: I 535 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: I 584 GLU cc_start: 0.8337 (tt0) cc_final: 0.8119 (tm-30) REVERT: I 601 LYS cc_start: 0.9342 (pttm) cc_final: 0.8813 (pttt) REVERT: I 625 ASN cc_start: 0.8819 (m-40) cc_final: 0.8473 (t0) REVERT: R 105 GLU cc_start: 0.7027 (pp20) cc_final: 0.6566 (tm-30) REVERT: N 42 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8364 (mmmm) REVERT: K 34 MET cc_start: 0.8585 (mmm) cc_final: 0.7866 (mmm) REVERT: K 85 GLU cc_start: 0.9214 (tp30) cc_final: 0.8799 (mp0) REVERT: K 100 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8233 (t0) REVERT: K 110 THR cc_start: 0.8521 (m) cc_final: 0.7999 (p) outliers start: 93 outliers final: 63 residues processed: 349 average time/residue: 0.1777 time to fit residues: 97.2411 Evaluate side-chains 331 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 259 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 238 optimal weight: 2.9990 chunk 235 optimal weight: 0.0570 chunk 130 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN E 195 ASN O 81 GLN M 90 HIS F 195 ASN P 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059572 restraints weight = 91165.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061989 restraints weight = 44512.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063589 restraints weight = 29584.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064589 restraints weight = 23213.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065138 restraints weight = 20073.562| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26541 Z= 0.128 Angle : 0.719 10.394 36354 Z= 0.350 Chirality : 0.044 0.190 4602 Planarity : 0.004 0.071 4233 Dihedral : 5.083 28.941 3243 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 2.00 % Allowed : 15.32 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.23 (0.15), residues: 2967 helix: 0.49 (0.28), residues: 369 sheet: 0.31 (0.17), residues: 939 loop : -0.54 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 61 TYR 0.016 0.001 TYR R 49 PHE 0.015 0.002 PHE R 98 TRP 0.026 0.002 TRP H 36 HIS 0.007 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (26313) covalent geometry : angle 0.69639 / 0.35 (35712) SS BOND : bond 0.00282 / 0.21 ( 42) SS BOND : angle 1.32928 / 0.89 ( 84) hydrogen bonds : bond 0.03865 / 2.59 ( 909) hydrogen bonds : angle 5.68397 / 3.96 ( 2421) link_ALPHA1-2 : bond 0.00496 / 0.29 ( 24) link_ALPHA1-2 : angle 1.70662 / 1.20 ( 72) link_ALPHA1-3 : bond 0.00525 / 0.34 ( 30) link_ALPHA1-3 : angle 1.63446 / 1.10 ( 90) link_ALPHA1-6 : bond 0.00732 / 0.45 ( 30) link_ALPHA1-6 : angle 1.65259 / 1.09 ( 90) link_BETA1-4 : bond 0.00327 / 0.21 ( 51) link_BETA1-4 : angle 1.32982 / 0.88 ( 153) link_NAG-ASN : bond 0.00230 / 0.15 ( 51) link_NAG-ASN : angle 1.49261 / 0.98 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 0.931 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 104 MET cc_start: 0.8801 (tpp) cc_final: 0.8071 (tpp) REVERT: A 426 MET cc_start: 0.8458 (tpt) cc_final: 0.8218 (tpt) REVERT: B 651 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7856 (p0) REVERT: L 79 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7508 (tm-30) REVERT: L 105 GLU cc_start: 0.6975 (tp30) cc_final: 0.6103 (pm20) REVERT: H 36 TRP cc_start: 0.7945 (m100) cc_final: 0.7576 (m100) REVERT: H 68 THR cc_start: 0.8928 (m) cc_final: 0.8583 (p) REVERT: H 72 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: D 30 GLU cc_start: 0.8968 (mp0) cc_final: 0.8451 (pm20) REVERT: D 39 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7426 (mmtm) REVERT: D 103 ARG cc_start: 0.8807 (ptp90) cc_final: 0.8348 (mpp-170) REVERT: C 11 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8095 (tp) REVERT: C 34 MET cc_start: 0.8567 (mmm) cc_final: 0.7932 (mmm) REVERT: C 100 ASN cc_start: 0.7679 (m-40) cc_final: 0.6593 (t0) REVERT: C 110 THR cc_start: 0.8182 (m) cc_final: 0.7584 (p) REVERT: E 434 MET cc_start: 0.8542 (ttp) cc_final: 0.7897 (ttp) REVERT: G 535 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7214 (mmt) REVERT: G 542 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7370 (mtt-85) REVERT: G 625 ASN cc_start: 0.8826 (m-40) cc_final: 0.8528 (m-40) REVERT: G 649 SER cc_start: 0.8867 (m) cc_final: 0.8564 (p) REVERT: Q 4 MET cc_start: 0.7952 (ttp) cc_final: 0.7746 (tmm) REVERT: Q 48 ILE cc_start: 0.8238 (mm) cc_final: 0.7974 (mp) REVERT: Q 105 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6298 (pm20) REVERT: O 68 THR cc_start: 0.8915 (m) cc_final: 0.8534 (p) REVERT: O 72 ASP cc_start: 0.7951 (t0) cc_final: 0.7555 (m-30) REVERT: M 42 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8490 (mmmm) REVERT: M 70 GLU cc_start: 0.9091 (pp20) cc_final: 0.8613 (pm20) REVERT: M 103 ARG cc_start: 0.8780 (mpp-170) cc_final: 0.8107 (tpp80) REVERT: J 11 LEU cc_start: 0.8580 (mp) cc_final: 0.8008 (tp) REVERT: J 79 TYR cc_start: 0.8598 (m-80) cc_final: 0.8345 (m-10) REVERT: J 100 LEU cc_start: 0.7820 (mt) cc_final: 0.7421 (mm) REVERT: J 110 THR cc_start: 0.8273 (m) cc_final: 0.7997 (p) REVERT: F 150 MET cc_start: 0.7894 (mtp) cc_final: 0.7537 (mtt) REVERT: F 271 MET cc_start: 0.8053 (mmm) cc_final: 0.7674 (mmm) REVERT: I 535 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7454 (mmm) REVERT: I 601 LYS cc_start: 0.9205 (pttm) cc_final: 0.8682 (pttm) REVERT: I 647 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7600 (mm-30) REVERT: I 652 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8631 (pp30) REVERT: R 24 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8212 (ttp80) REVERT: R 105 GLU cc_start: 0.7130 (pp20) cc_final: 0.6715 (tm-30) REVERT: N 4 MET cc_start: 0.4293 (OUTLIER) cc_final: 0.3939 (ppp) REVERT: N 30 GLU cc_start: 0.8817 (mp0) cc_final: 0.8481 (pm20) REVERT: N 42 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8464 (mmmm) REVERT: N 45 LYS cc_start: 0.7529 (mptt) cc_final: 0.7262 (mmtt) REVERT: K 34 MET cc_start: 0.8594 (mmm) cc_final: 0.7867 (mmm) REVERT: K 98 ASP cc_start: 0.8756 (m-30) cc_final: 0.8553 (m-30) REVERT: K 100 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7858 (t0) REVERT: K 110 THR cc_start: 0.8440 (m) cc_final: 0.7920 (p) outliers start: 52 outliers final: 37 residues processed: 334 average time/residue: 0.1845 time to fit residues: 95.8105 Evaluate side-chains 315 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 11 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 272 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN E 195 ASN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN P 81 GLN P 82AHIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.083416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058480 restraints weight = 91181.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060824 restraints weight = 45274.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.062376 restraints weight = 30393.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063346 restraints weight = 24012.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063928 restraints weight = 20837.752| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26541 Z= 0.175 Angle : 0.742 10.839 36354 Z= 0.361 Chirality : 0.044 0.191 4602 Planarity : 0.005 0.068 4233 Dihedral : 5.096 30.158 3243 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 1.96 % Allowed : 15.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.36 (0.15), residues: 2967 helix: 0.43 (0.28), residues: 372 sheet: 0.17 (0.17), residues: 990 loop : -0.61 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 83 TYR 0.016 0.001 TYR Q 49 PHE 0.016 0.002 PHE O 27 TRP 0.047 0.002 TRP M 35 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (26313) covalent geometry : angle 0.71756 / 0.36 (35712) SS BOND : bond 0.00302 / 0.21 ( 42) SS BOND : angle 1.28407 / 0.87 ( 84) hydrogen bonds : bond 0.03980 / 2.65 ( 909) hydrogen bonds : angle 5.72446 / 3.99 ( 2421) link_ALPHA1-2 : bond 0.00229 / 0.13 ( 24) link_ALPHA1-2 : angle 1.96011 / 1.36 ( 72) link_ALPHA1-3 : bond 0.00483 / 0.31 ( 30) link_ALPHA1-3 : angle 1.62910 / 1.09 ( 90) link_ALPHA1-6 : bond 0.00669 / 0.40 ( 30) link_ALPHA1-6 : angle 1.69199 / 1.13 ( 90) link_BETA1-4 : bond 0.00300 / 0.19 ( 51) link_BETA1-4 : angle 1.44822 / 0.97 ( 153) link_NAG-ASN : bond 0.00367 / 0.22 ( 51) link_NAG-ASN : angle 1.63993 / 1.10 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 1.133 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 104 MET cc_start: 0.8841 (tpp) cc_final: 0.8161 (tpp) REVERT: A 161 MET cc_start: 0.9000 (tpt) cc_final: 0.8545 (tpt) REVERT: B 584 GLU cc_start: 0.8613 (tt0) cc_final: 0.8223 (tm-30) REVERT: B 601 LYS cc_start: 0.9139 (pttt) cc_final: 0.8830 (mttt) REVERT: B 651 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7887 (p0) REVERT: L 55 LYS cc_start: 0.7917 (tttt) cc_final: 0.7444 (ptmt) REVERT: L 79 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7506 (tm-30) REVERT: L 105 GLU cc_start: 0.6950 (tp30) cc_final: 0.6129 (pm20) REVERT: L 106 ILE cc_start: 0.6419 (tp) cc_final: 0.5651 (tp) REVERT: H 72 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: H 79 TYR cc_start: 0.7979 (m-80) cc_final: 0.7462 (m-10) REVERT: D 30 GLU cc_start: 0.8825 (mp0) cc_final: 0.8365 (pm20) REVERT: D 39 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7444 (mmtm) REVERT: D 82 ASP cc_start: 0.7915 (m-30) cc_final: 0.7690 (m-30) REVERT: D 103 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8107 (mpp-170) REVERT: C 34 MET cc_start: 0.8606 (mmm) cc_final: 0.7994 (mmm) REVERT: C 100 ASN cc_start: 0.7740 (m-40) cc_final: 0.6709 (t0) REVERT: E 434 MET cc_start: 0.8575 (ttp) cc_final: 0.7997 (ttp) REVERT: G 535 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7223 (mmt) REVERT: G 542 ARG cc_start: 0.7990 (ttt-90) cc_final: 0.7488 (mtt-85) REVERT: Q 4 MET cc_start: 0.7915 (ttp) cc_final: 0.7691 (tmm) REVERT: O 68 THR cc_start: 0.8942 (m) cc_final: 0.8572 (p) REVERT: O 72 ASP cc_start: 0.7922 (t0) cc_final: 0.7347 (m-30) REVERT: O 100 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8301 (t0) REVERT: M 39 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7248 (mmtm) REVERT: M 103 ARG cc_start: 0.8802 (mpp-170) cc_final: 0.8149 (tpp80) REVERT: J 11 LEU cc_start: 0.8575 (mp) cc_final: 0.8006 (tp) REVERT: J 110 THR cc_start: 0.8296 (m) cc_final: 0.8004 (p) REVERT: F 271 MET cc_start: 0.8103 (mmm) cc_final: 0.7649 (mmm) REVERT: I 535 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7728 (mmt) REVERT: I 584 GLU cc_start: 0.8377 (tt0) cc_final: 0.8173 (tm-30) REVERT: I 601 LYS cc_start: 0.9263 (pttm) cc_final: 0.8753 (pttm) REVERT: I 647 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7796 (mm-30) REVERT: R 24 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8238 (ttp80) REVERT: R 105 GLU cc_start: 0.7124 (pp20) cc_final: 0.6796 (tm-30) REVERT: N 30 GLU cc_start: 0.8803 (mp0) cc_final: 0.8459 (pm20) REVERT: N 42 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8439 (mmmm) REVERT: N 45 LYS cc_start: 0.7542 (mptt) cc_final: 0.7276 (mmtt) REVERT: K 34 MET cc_start: 0.8582 (mmm) cc_final: 0.7896 (mmm) REVERT: K 100 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8036 (t0) REVERT: K 110 THR cc_start: 0.8439 (m) cc_final: 0.7904 (p) outliers start: 51 outliers final: 37 residues processed: 312 average time/residue: 0.1788 time to fit residues: 87.0462 Evaluate side-chains 309 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 69 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 61 optimal weight: 30.0000 chunk 277 optimal weight: 0.4980 chunk 281 optimal weight: 30.0000 chunk 265 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN H 3 GLN E 195 ASN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058353 restraints weight = 91061.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060636 restraints weight = 46072.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.062149 restraints weight = 31259.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063110 restraints weight = 24825.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063700 restraints weight = 21560.762| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26541 Z= 0.184 Angle : 0.748 10.848 36354 Z= 0.363 Chirality : 0.045 0.185 4602 Planarity : 0.005 0.071 4233 Dihedral : 5.123 31.065 3243 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 2.19 % Allowed : 15.86 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.41 (0.15), residues: 2967 helix: 0.43 (0.28), residues: 372 sheet: 0.15 (0.17), residues: 990 loop : -0.67 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 83 TYR 0.018 0.001 TYR Q 91 PHE 0.013 0.002 PHE R 98 TRP 0.057 0.002 TRP M 35 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (26313) covalent geometry : angle 0.72263 / 0.36 (35712) SS BOND : bond 0.00324 / 0.24 ( 42) SS BOND : angle 1.40870 / 0.93 ( 84) hydrogen bonds : bond 0.04002 / 2.67 ( 909) hydrogen bonds : angle 5.68991 / 3.97 ( 2421) link_ALPHA1-2 : bond 0.00247 / 0.15 ( 24) link_ALPHA1-2 : angle 1.96465 / 1.36 ( 72) link_ALPHA1-3 : bond 0.00462 / 0.30 ( 30) link_ALPHA1-3 : angle 1.64083 / 1.10 ( 90) link_ALPHA1-6 : bond 0.00659 / 0.40 ( 30) link_ALPHA1-6 : angle 1.69395 / 1.13 ( 90) link_BETA1-4 : bond 0.00299 / 0.18 ( 51) link_BETA1-4 : angle 1.43967 / 0.96 ( 153) link_NAG-ASN : bond 0.00372 / 0.23 ( 51) link_NAG-ASN : angle 1.66066 / 1.11 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.83 seconds wall clock time: 87 minutes 3.81 seconds (5223.81 seconds total)