Starting phenix.real_space_refine on Sat Jul 4 10:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpi_34193/07_2026/8gpi_34193.cif" } resolution = 3.0 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= 0.002 sd= 0.030 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 117 5.16 5 C 12666 2.51 5 N 3297 2.21 5 O 4185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20265 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "S" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "T" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "X" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "Y" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "Z" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3408 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.00, per 1000 atoms: 0.20 Number of scatterers: 20265 At special positions: 0 Unit cell: (150.52, 155.82, 126.14, 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 117 16.00 O 4185 8.00 N 3297 7.00 C 12666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 605 " - pdb=" SG CYS X 501 " distance=2.03 Simple disulfide: pdb=" SG CYS S 598 " - pdb=" SG CYS S 604 " distance=2.03 Simple disulfide: pdb=" SG CYS S 605 " - pdb=" SG CYS Y 501 " distance=2.03 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 Simple disulfide: pdb=" SG CYS T 605 " - pdb=" SG CYS Z 501 " distance=2.03 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 119 " - pdb=" SG CYS X 205 " distance=2.03 Simple disulfide: pdb=" SG CYS X 126 " - pdb=" SG CYS X 196 " distance=2.03 Simple disulfide: pdb=" SG CYS X 131 " - pdb=" SG CYS X 157 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.05 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 119 " - pdb=" SG CYS Y 205 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 126 " - pdb=" SG CYS Y 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 131 " - pdb=" SG CYS Y 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 218 " - pdb=" SG CYS Y 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 296 " - pdb=" SG CYS Y 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 126 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 131 " - pdb=" SG CYS Z 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 218 " - pdb=" SG CYS Z 247 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 228 " - pdb=" SG CYS Z 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 296 " - pdb=" SG CYS Z 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 378 " - pdb=" SG CYS Z 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 385 " - pdb=" SG CYS Z 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN K 10 " - " MAN K 11 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN b 10 " - " MAN b 11 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN k 8 " - " MAN k 9 " " MAN k 10 " - " MAN k 11 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA M 3 " - " MAN M 4 " " BMA b 3 " - " MAN b 4 " " MAN b 7 " - " MAN b 8 " " BMA c 3 " - " MAN c 4 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 8 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 10 " " BMA M 3 " - " MAN M 5 " " BMA b 3 " - " MAN b 7 " " MAN b 7 " - " MAN b 10 " " BMA c 3 " - " MAN c 5 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 10 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG B 1 " - " ASN R 637 " " NAG F 1 " - " ASN S 637 " " NAG G 1 " - " ASN T 637 " " NAG I 1 " - " ASN X 156 " " NAG J 1 " - " ASN X 197 " " NAG K 1 " - " ASN X 234 " " NAG M 1 " - " ASN X 262 " " NAG N 1 " - " ASN X 444 " " NAG O 1 " - " ASN X 386 " " NAG P 1 " - " ASN X 276 " " NAG Q 1 " - " ASN X 289 " " NAG R 701 " - " ASN R 611 " " NAG S 701 " - " ASN S 611 " " NAG T 701 " - " ASN T 611 " " NAG U 1 " - " ASN X 339 " " NAG V 1 " - " ASN X 130 " " NAG W 1 " - " ASN Y 156 " " NAG X 701 " - " ASN X 88 " " NAG X 702 " - " ASN X 135 " " NAG X 703 " - " ASN X 149 " " NAG X 704 " - " ASN X 160 " " NAG X 705 " - " ASN X 241 " " NAG X 706 " - " ASN X 448 " " NAG X 707 " - " ASN X 301 " " NAG X 708 " - " ASN X 334 " " NAG Y 701 " - " ASN Y 88 " " NAG Y 702 " - " ASN Y 135 " " NAG Y 703 " - " ASN Y 149 " " NAG Y 704 " - " ASN Y 160 " " NAG Y 705 " - " ASN Y 241 " " NAG Y 706 " - " ASN Y 301 " " NAG Y 707 " - " ASN Y 334 " " NAG Y 708 " - " ASN Y 339 " " NAG Y 709 " - " ASN Y 448 " " NAG Z 701 " - " ASN Z 88 " " NAG Z 702 " - " ASN Z 135 " " NAG Z 703 " - " ASN Z 149 " " NAG Z 704 " - " ASN Z 160 " " NAG Z 705 " - " ASN Z 241 " " NAG Z 706 " - " ASN Z 448 " " NAG Z 707 " - " ASN Z 301 " " NAG Z 708 " - " ASN Z 334 " " NAG Z 709 " - " ASN Z 356 " " NAG a 1 " - " ASN Y 197 " " NAG b 1 " - " ASN Y 234 " " NAG c 1 " - " ASN Y 262 " " NAG d 1 " - " ASN Y 276 " " NAG e 1 " - " ASN Y 289 " " NAG f 1 " - " ASN Y 386 " " NAG g 1 " - " ASN Y 444 " " NAG h 1 " - " ASN Y 130 " " NAG i 1 " - " ASN Z 156 " " NAG j 1 " - " ASN Z 197 " " NAG k 1 " - " ASN Z 234 " " NAG l 1 " - " ASN Z 262 " " NAG m 1 " - " ASN Z 276 " " NAG n 1 " - " ASN Z 289 " " NAG o 1 " - " ASN Z 339 " " NAG p 1 " - " ASN Z 386 " " NAG q 1 " - " ASN Z 444 " " NAG r 1 " - " ASN Z 130 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 791.3 milliseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 38 sheets defined 19.1% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.978A pdb=" N THR A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.599A pdb=" N PHE C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.563A pdb=" N ARG D 63 " --> pdb=" O HIS D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.029A pdb=" N THR D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.584A pdb=" N PHE E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.079A pdb=" N THR H 93 " --> pdb=" O SER H 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 536 through 544 removed outlier: 4.308A pdb=" N GLN R 540 " --> pdb=" O THR R 536 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN R 543 " --> pdb=" O VAL R 539 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU R 544 " --> pdb=" O GLN R 540 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 596 removed outlier: 3.701A pdb=" N TRP R 596 " --> pdb=" O PHE R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 625 Processing helix chain 'R' and resid 627 through 635 Processing helix chain 'R' and resid 638 through 663 Processing helix chain 'S' and resid 529 through 534 Processing helix chain 'S' and resid 537 through 544 removed outlier: 3.562A pdb=" N ALA S 541 " --> pdb=" O LEU S 537 " (cutoff:3.500A) Processing helix chain 'S' and resid 572 through 596 removed outlier: 3.662A pdb=" N TRP S 596 " --> pdb=" O PHE S 592 " (cutoff:3.500A) Processing helix chain 'S' and resid 618 through 625 Processing helix chain 'S' and resid 627 through 635 Processing helix chain 'S' and resid 638 through 663 Processing helix chain 'T' and resid 529 through 534 Processing helix chain 'T' and resid 538 through 544 Processing helix chain 'T' and resid 572 through 596 removed outlier: 3.600A pdb=" N TRP T 596 " --> pdb=" O PHE T 592 " (cutoff:3.500A) Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 663 removed outlier: 3.588A pdb=" N ASP T 644 " --> pdb=" O ASN T 640 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 117 removed outlier: 4.287A pdb=" N GLU X 102 " --> pdb=" O ASN X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 126 removed outlier: 3.667A pdb=" N CYS X 126 " --> pdb=" O THR X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 198 Processing helix chain 'X' and resid 335 through 350 Processing helix chain 'X' and resid 476 through 481 removed outlier: 3.748A pdb=" N SER X 481 " --> pdb=" O ASP X 477 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 116 removed outlier: 4.471A pdb=" N GLU Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 126 removed outlier: 3.662A pdb=" N CYS Y 126 " --> pdb=" O THR Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 350 Processing helix chain 'Y' and resid 368 through 373 removed outlier: 3.567A pdb=" N THR Y 372 " --> pdb=" O ASP Y 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET Y 373 " --> pdb=" O LEU Y 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 368 through 373' Processing helix chain 'Y' and resid 476 through 484 removed outlier: 3.639A pdb=" N SER Y 481 " --> pdb=" O ASP Y 477 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU Y 482 " --> pdb=" O ASN Y 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 116 removed outlier: 4.378A pdb=" N GLU Z 102 " --> pdb=" O ASN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 123 through 126 removed outlier: 3.615A pdb=" N CYS Z 126 " --> pdb=" O THR Z 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 123 through 126' Processing helix chain 'Z' and resid 149 through 152 removed outlier: 4.367A pdb=" N ASP Z 152 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 149 through 152' Processing helix chain 'Z' and resid 195 through 198 Processing helix chain 'Z' and resid 335 through 350 Processing helix chain 'Z' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR Z 372 " --> pdb=" O ASP Z 368 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Z 373 " --> pdb=" O LEU Z 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 368 through 373' Processing helix chain 'Z' and resid 475 through 484 removed outlier: 3.685A pdb=" N TRP Z 479 " --> pdb=" O ILE Z 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Z 482 " --> pdb=" O ASN Z 478 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR Z 484 " --> pdb=" O ARG Z 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 9 through 10 current: chain 'A' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 55 through 58 current: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.639A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'D' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 10 current: chain 'D' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 55 through 58 current: chain 'D' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'D' and resid 111 through 112 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 9 through 10 current: chain 'E' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 53 through 54 current: chain 'E' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 10 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 55 through 58 current: chain 'H' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'H' and resid 111 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 33 through 38 removed outlier: 6.364A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'R' and resid 603 through 609 removed outlier: 5.111A pdb=" N VAL X 36 " --> pdb=" O THR R 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 603 through 609 removed outlier: 5.426A pdb=" N VAL Y 36 " --> pdb=" O THR S 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 603 through 609 removed outlier: 4.940A pdb=" N VAL Z 36 " --> pdb=" O THR T 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 45 through 47 removed outlier: 4.409A pdb=" N VAL X 242 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'X' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'X' and resid 201 through 203 removed outlier: 6.544A pdb=" N LYS X 202 " --> pdb=" O TYR X 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 259 through 261 current: chain 'X' and resid 284 through 298 removed outlier: 7.446A pdb=" N SER X 293 " --> pdb=" O ASN X 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN X 334 " --> pdb=" O SER X 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 330 through 334 current: chain 'X' and resid 381 through 385 removed outlier: 4.035A pdb=" N PHE X 382 " --> pdb=" O LYS X 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 413 through 421 current: chain 'X' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'X' and resid 302 through 312 removed outlier: 6.887A pdb=" N THR X 303 " --> pdb=" O GLY X 320A" (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN X 315 " --> pdb=" O ILE X 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 45 through 47 removed outlier: 4.609A pdb=" N VAL Y 242 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'Y' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'Y' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'Y' and resid 202 through 203 removed outlier: 6.474A pdb=" N LYS Y 202 " --> pdb=" O TYR Y 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 259 through 261 current: chain 'Y' and resid 284 through 298 removed outlier: 7.370A pdb=" N SER Y 293 " --> pdb=" O ASN Y 334 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN Y 334 " --> pdb=" O SER Y 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 329 through 334 current: chain 'Y' and resid 381 through 385 removed outlier: 4.274A pdb=" N PHE Y 382 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 413 through 421 current: chain 'Y' and resid 465 through 470 Processing sheet with id=AD5, first strand: chain 'Y' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'Z' and resid 45 through 47 removed outlier: 4.575A pdb=" N VAL Z 242 " --> pdb=" O LEU Z 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'Z' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'Z' and resid 120 through 121 removed outlier: 3.927A pdb=" N VAL Z 120 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS Z 202 " --> pdb=" O TYR Z 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'Z' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 259 through 261 current: chain 'Z' and resid 284 through 312 removed outlier: 6.362A pdb=" N GLY Z 324 " --> pdb=" O PRO Z 299 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN Z 301 " --> pdb=" O ILE Z 322 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE Z 322 " --> pdb=" O ASN Z 301 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR Z 303 " --> pdb=" O GLY Z 320A" (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN Z 315 " --> pdb=" O ILE Z 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 315 through 324 current: chain 'Z' and resid 381 through 385 removed outlier: 4.248A pdb=" N PHE Z 382 " --> pdb=" O LYS Z 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 413 through 421 current: chain 'Z' and resid 465 through 470 570 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6234 1.35 - 1.48: 5542 1.48 - 1.61: 8732 1.61 - 1.74: 0 1.74 - 1.86: 156 Bond restraints: 20664 Sorted by residual: bond pdb=" C1 MAN b 5 " pdb=" C2 MAN b 5 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 MAN c 4 " pdb=" C2 MAN c 4 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN K 5 " pdb=" C2 MAN K 5 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 MAN k 5 " pdb=" C2 MAN k 5 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C2 BMA K 3 " pdb=" C3 BMA K 3 " ideal model delta sigma weight residual 1.544 1.506 0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 20659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27075 1.88 - 3.76: 790 3.76 - 5.65: 130 5.65 - 7.53: 56 7.53 - 9.41: 5 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C GLN Z 432 " pdb=" CA GLN Z 432 " pdb=" CB GLN Z 432 " ideal model delta sigma weight residual 117.23 110.56 6.67 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CA CYS X 247 " pdb=" CB CYS X 247 " pdb=" SG CYS X 247 " ideal model delta sigma weight residual 114.40 123.81 -9.41 2.30e+00 1.89e-01 1.67e+01 angle pdb=" CA CYS Z 247 " pdb=" CB CYS Z 247 " pdb=" SG CYS Z 247 " ideal model delta sigma weight residual 114.40 123.23 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA GLN Z 432 " pdb=" C GLN Z 432 " pdb=" N ALA Z 433 " ideal model delta sigma weight residual 119.98 116.89 3.09 8.50e-01 1.38e+00 1.32e+01 angle pdb=" CA PRO X 206 " pdb=" N PRO X 206 " pdb=" CD PRO X 206 " ideal model delta sigma weight residual 112.00 107.35 4.65 1.40e+00 5.10e-01 1.10e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10557 17.91 - 35.83: 616 35.83 - 53.74: 110 53.74 - 71.66: 27 71.66 - 89.57: 24 Dihedral angle restraints: 11334 sinusoidal: 4554 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS X 54 " pdb=" SG CYS X 54 " pdb=" SG CYS X 74 " pdb=" CB CYS X 74 " ideal model delta sinusoidal sigma weight residual 93.00 20.15 72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS Z 378 " pdb=" SG CYS Z 378 " pdb=" SG CYS Z 445 " pdb=" CB CYS Z 445 " ideal model delta sinusoidal sigma weight residual -86.00 -157.87 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS Y 378 " pdb=" SG CYS Y 378 " pdb=" SG CYS Y 445 " pdb=" CB CYS Y 445 " ideal model delta sinusoidal sigma weight residual -86.00 -155.58 69.58 1 1.00e+01 1.00e-02 6.25e+01 ... (remaining 11331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2839 0.058 - 0.116: 596 0.116 - 0.174: 101 0.174 - 0.231: 0 0.231 - 0.289: 10 Chirality restraints: 3546 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN Z 444 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA k 3 " pdb=" C4 BMA k 3 " pdb=" C6 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3543 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS X 205 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO X 206 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO X 206 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO X 206 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 75 " 0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO Y 76 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO Y 76 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO Y 76 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 32 " 0.016 2.00e-02 2.50e+03 1.45e-02 5.26e+00 pdb=" CG TRP L 32 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 32 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP L 32 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 32 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 32 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 32 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 32 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 32 " 0.004 2.00e-02 2.50e+03 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1026 2.73 - 3.27: 18705 3.27 - 3.82: 32183 3.82 - 4.36: 37999 4.36 - 4.90: 67032 Nonbonded interactions: 156945 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" OG SER A 82 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR X 37 " pdb=" OG1 THR X 499 " model vdw 2.208 3.040 nonbonded pdb=" OG SER H 69 " pdb=" OG SER H 82 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR A 74 " pdb=" OG SER A 77 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLU D 84 " pdb=" O4 MAN K 6 " model vdw 2.263 3.040 ... (remaining 156940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'b' selection = chain 'k' } ncs_group { reference = chain 'M' selection = chain 'c' selection = chain 'l' } ncs_group { reference = chain 'P' selection = chain 'd' selection = chain 'm' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 33 through 708) selection = (chain 'Z' and resid 33 through 708) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.560 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20834 Z= 0.248 Angle : 0.795 9.409 28528 Z= 0.356 Chirality : 0.050 0.289 3546 Planarity : 0.005 0.100 3375 Dihedral : 12.446 89.572 6858 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2316 helix: 1.41 (0.28), residues: 384 sheet: 0.96 (0.20), residues: 666 loop : -0.33 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG X 166 TYR 0.022 0.001 TYR L 91 PHE 0.024 0.002 PHE R 522 TRP 0.038 0.002 TRP L 32 HIS 0.007 0.001 HIS Y 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (20664) covalent geometry : angle 0.76121 / 0.35 (28056) SS BOND : bond 0.00470 / 0.23 ( 38) SS BOND : angle 1.62326 / 1.22 ( 76) hydrogen bonds : bond 0.12412 / 8.07 ( 570) hydrogen bonds : angle 5.68932 / 3.96 ( 1533) link_ALPHA1-2 : bond 0.00270 / 0.16 ( 12) link_ALPHA1-2 : angle 1.76673 / 1.25 ( 36) link_ALPHA1-3 : bond 0.00384 / 0.19 ( 9) link_ALPHA1-3 : angle 1.61489 / 1.08 ( 27) link_ALPHA1-6 : bond 0.00191 / 0.09 ( 9) link_ALPHA1-6 : angle 2.09288 / 1.35 ( 27) link_BETA1-4 : bond 0.00584 / 0.44 ( 41) link_BETA1-4 : angle 1.86249 / 1.25 ( 123) link_NAG-ASN : bond 0.00293 / 0.20 ( 61) link_NAG-ASN : angle 2.15374 / 1.53 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.672 Fit side-chains REVERT: D 116 MET cc_start: 0.8146 (mtp) cc_final: 0.7941 (mtm) REVERT: H 110 LEU cc_start: 0.8619 (mt) cc_final: 0.8403 (mt) REVERT: X 211 ASP cc_start: 0.7264 (t0) cc_final: 0.7059 (t0) REVERT: X 326 ILE cc_start: 0.8364 (mm) cc_final: 0.8109 (mp) REVERT: X 457 ASP cc_start: 0.7378 (t0) cc_final: 0.7158 (t0) REVERT: X 466 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7139 (tp30) REVERT: Y 111 LEU cc_start: 0.8044 (tt) cc_final: 0.7829 (tp) REVERT: Y 207 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7260 (mtmm) REVERT: Y 231 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7472 (mtpp) REVERT: Y 347 GLU cc_start: 0.7255 (tp30) cc_final: 0.6985 (tp30) REVERT: Y 443 ILE cc_start: 0.8399 (mm) cc_final: 0.8172 (mp) REVERT: Y 477 ASP cc_start: 0.7908 (m-30) cc_final: 0.7678 (m-30) REVERT: Z 123 THR cc_start: 0.8421 (t) cc_final: 0.8182 (p) REVERT: Z 168 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7916 (mmmm) REVERT: Z 211 ASP cc_start: 0.7379 (t0) cc_final: 0.7179 (t0) REVERT: Z 240 LYS cc_start: 0.7675 (mppt) cc_final: 0.7416 (mtmm) outliers start: 0 outliers final: 1 residues processed: 403 average time/residue: 0.6469 time to fit residues: 292.1688 Evaluate side-chains 375 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN X 114 GLN X 425 ASN Y 105 GLN Y 375 HIS Z 98 ASN Z 169 GLN Z 315 GLN Z 343 ASN Z 474 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102052 restraints weight = 29922.828| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.50 r_work: 0.3164 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20834 Z= 0.208 Angle : 0.631 9.085 28528 Z= 0.306 Chirality : 0.044 0.185 3546 Planarity : 0.005 0.083 3375 Dihedral : 4.529 30.319 2516 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 7.90 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.17), residues: 2316 helix: 1.79 (0.27), residues: 387 sheet: 0.85 (0.19), residues: 711 loop : -0.28 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 327 TYR 0.021 0.002 TYR E 91 PHE 0.016 0.002 PHE Y 176 TRP 0.016 0.002 TRP C 32 HIS 0.009 0.001 HIS Y 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (20664) covalent geometry : angle 0.59290 / 0.30 (28056) SS BOND : bond 0.00399 / 0.23 ( 38) SS BOND : angle 1.51762 / 1.15 ( 76) hydrogen bonds : bond 0.05250 / 3.45 ( 570) hydrogen bonds : angle 4.72810 / 3.30 ( 1533) link_ALPHA1-2 : bond 0.00322 / 0.19 ( 12) link_ALPHA1-2 : angle 1.83286 / 1.33 ( 36) link_ALPHA1-3 : bond 0.00531 / 0.26 ( 9) link_ALPHA1-3 : angle 1.53168 / 1.05 ( 27) link_ALPHA1-6 : bond 0.00251 / 0.12 ( 9) link_ALPHA1-6 : angle 1.71745 / 1.13 ( 27) link_BETA1-4 : bond 0.00426 / 0.31 ( 41) link_BETA1-4 : angle 1.55250 / 1.05 ( 123) link_NAG-ASN : bond 0.00362 / 0.25 ( 61) link_NAG-ASN : angle 2.05564 / 1.45 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 390 time to evaluate : 0.756 Fit side-chains REVERT: A 125 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8227 (p) REVERT: H 110 LEU cc_start: 0.8838 (mt) cc_final: 0.8626 (mt) REVERT: L 58 VAL cc_start: 0.7772 (t) cc_final: 0.7475 (p) REVERT: R 624 ASN cc_start: 0.8235 (m110) cc_final: 0.7977 (m-40) REVERT: S 606 THR cc_start: 0.8603 (t) cc_final: 0.8370 (p) REVERT: T 610 TRP cc_start: 0.8389 (t-100) cc_final: 0.8175 (t-100) REVERT: X 211 ASP cc_start: 0.7797 (t0) cc_final: 0.7517 (t0) REVERT: X 232 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8380 (mtmm) REVERT: X 457 ASP cc_start: 0.8056 (t0) cc_final: 0.7734 (t0) REVERT: X 466 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7619 (tp30) REVERT: Y 207 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7595 (mtmm) REVERT: Y 231 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7786 (mtpp) REVERT: Y 347 GLU cc_start: 0.8132 (tp30) cc_final: 0.7739 (tp30) REVERT: Y 477 ASP cc_start: 0.8445 (m-30) cc_final: 0.8238 (m-30) REVERT: Z 103 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: Z 105 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7685 (tp40) REVERT: Z 168 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8242 (mmmm) REVERT: Z 211 ASP cc_start: 0.7858 (t0) cc_final: 0.7622 (t0) REVERT: Z 426 MET cc_start: 0.6340 (mtt) cc_final: 0.5673 (mtt) outliers start: 41 outliers final: 19 residues processed: 401 average time/residue: 0.6269 time to fit residues: 284.0559 Evaluate side-chains 399 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 377 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 208 ILE Chi-restraints excluded: chain Y residue 290 LYS Chi-restraints excluded: chain Y residue 443 ILE Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 23 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 209 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 GLN X 425 ASN Y 375 HIS Z 169 GLN Z 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102051 restraints weight = 30094.017| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.52 r_work: 0.3169 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20834 Z= 0.157 Angle : 0.581 7.985 28528 Z= 0.284 Chirality : 0.043 0.180 3546 Planarity : 0.004 0.084 3375 Dihedral : 4.370 31.987 2514 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.57 % Allowed : 9.93 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2316 helix: 1.99 (0.27), residues: 387 sheet: 0.79 (0.19), residues: 714 loop : -0.21 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 166 TYR 0.017 0.001 TYR E 91 PHE 0.012 0.001 PHE Y 176 TRP 0.015 0.001 TRP C 32 HIS 0.009 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (20664) covalent geometry : angle 0.54540 / 0.28 (28056) SS BOND : bond 0.00389 / 0.25 ( 38) SS BOND : angle 1.46912 / 1.12 ( 76) hydrogen bonds : bond 0.04656 / 3.08 ( 570) hydrogen bonds : angle 4.55053 / 3.17 ( 1533) link_ALPHA1-2 : bond 0.00336 / 0.20 ( 12) link_ALPHA1-2 : angle 1.56083 / 1.14 ( 36) link_ALPHA1-3 : bond 0.00531 / 0.26 ( 9) link_ALPHA1-3 : angle 1.39820 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00160 / 0.07 ( 9) link_ALPHA1-6 : angle 1.62823 / 1.07 ( 27) link_BETA1-4 : bond 0.00423 / 0.31 ( 41) link_BETA1-4 : angle 1.44350 / 0.98 ( 123) link_NAG-ASN : bond 0.00248 / 0.17 ( 61) link_NAG-ASN : angle 1.87168 / 1.33 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 375 time to evaluate : 0.827 Fit side-chains REVERT: A 43 GLN cc_start: 0.7135 (mp10) cc_final: 0.5606 (mp10) REVERT: A 125 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8255 (p) REVERT: E 48 ILE cc_start: 0.8065 (mm) cc_final: 0.7828 (mp) REVERT: R 624 ASN cc_start: 0.8250 (m110) cc_final: 0.7968 (m-40) REVERT: S 626 MET cc_start: 0.8375 (mtp) cc_final: 0.8159 (mtm) REVERT: X 211 ASP cc_start: 0.7776 (t0) cc_final: 0.7508 (t0) REVERT: X 457 ASP cc_start: 0.8048 (t0) cc_final: 0.7723 (t0) REVERT: X 466 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7631 (tp30) REVERT: Y 207 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7628 (mtmm) REVERT: Y 231 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7749 (mtpp) REVERT: Y 347 GLU cc_start: 0.8159 (tp30) cc_final: 0.7749 (tp30) REVERT: Y 456 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7431 (ttm170) REVERT: Y 503 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7684 (mtm-85) REVERT: Z 107 ASP cc_start: 0.8116 (m-30) cc_final: 0.7915 (m-30) REVERT: Z 211 ASP cc_start: 0.7862 (t0) cc_final: 0.7617 (t0) REVERT: Z 321 ASP cc_start: 0.8061 (t0) cc_final: 0.7813 (t70) REVERT: Z 381 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7831 (mm-30) REVERT: Z 426 MET cc_start: 0.6398 (mtt) cc_final: 0.5710 (mtt) outliers start: 53 outliers final: 28 residues processed: 393 average time/residue: 0.6411 time to fit residues: 283.7620 Evaluate side-chains 404 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 373 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain T residue 589 ASP Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 127 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN H 43 GLN ** S 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN X 315 GLN X 425 ASN Y 375 HIS Z 169 GLN Z 343 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102782 restraints weight = 30327.934| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.46 r_work: 0.3179 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20834 Z= 0.112 Angle : 0.537 7.291 28528 Z= 0.262 Chirality : 0.042 0.216 3546 Planarity : 0.004 0.079 3375 Dihedral : 4.160 28.084 2514 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.66 % Allowed : 11.48 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.89 (0.18), residues: 2316 helix: 2.40 (0.28), residues: 369 sheet: 0.89 (0.19), residues: 711 loop : -0.11 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 166 TYR 0.013 0.001 TYR L 91 PHE 0.011 0.001 PHE X 53 TRP 0.016 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20664) covalent geometry : angle 0.50581 / 0.26 (28056) SS BOND : bond 0.00386 / 0.20 ( 38) SS BOND : angle 1.27907 / 0.97 ( 76) hydrogen bonds : bond 0.03986 / 2.64 ( 570) hydrogen bonds : angle 4.37131 / 3.04 ( 1533) link_ALPHA1-2 : bond 0.00369 / 0.22 ( 12) link_ALPHA1-2 : angle 1.51156 / 1.09 ( 36) link_ALPHA1-3 : bond 0.00553 / 0.26 ( 9) link_ALPHA1-3 : angle 1.35049 / 0.93 ( 27) link_ALPHA1-6 : bond 0.00204 / 0.09 ( 9) link_ALPHA1-6 : angle 1.56673 / 1.04 ( 27) link_BETA1-4 : bond 0.00423 / 0.31 ( 41) link_BETA1-4 : angle 1.35423 / 0.91 ( 123) link_NAG-ASN : bond 0.00163 / 0.12 ( 61) link_NAG-ASN : angle 1.67569 / 1.19 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 0.768 Fit side-chains REVERT: A 74 THR cc_start: 0.8284 (t) cc_final: 0.8053 (t) REVERT: A 100 THR cc_start: 0.8687 (m) cc_final: 0.8358 (t) REVERT: A 125 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8262 (p) REVERT: E 48 ILE cc_start: 0.8051 (mm) cc_final: 0.7844 (mp) REVERT: E 100 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: H 67 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7959 (tp) REVERT: R 624 ASN cc_start: 0.8294 (m110) cc_final: 0.7988 (m-40) REVERT: S 626 MET cc_start: 0.8392 (mtp) cc_final: 0.8154 (mtm) REVERT: X 211 ASP cc_start: 0.7784 (t0) cc_final: 0.7498 (t0) REVERT: X 457 ASP cc_start: 0.8020 (t0) cc_final: 0.7722 (t0) REVERT: Y 207 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7559 (mtmm) REVERT: Y 347 GLU cc_start: 0.8169 (tp30) cc_final: 0.7760 (tp30) REVERT: Y 426 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5630 (mtp) REVERT: Y 456 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7449 (ttm170) REVERT: Z 211 ASP cc_start: 0.7895 (t0) cc_final: 0.7641 (t0) REVERT: Z 321 ASP cc_start: 0.8068 (t0) cc_final: 0.7835 (t0) REVERT: Z 381 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7647 (mm-30) REVERT: Z 426 MET cc_start: 0.6314 (mtt) cc_final: 0.5662 (mtt) outliers start: 55 outliers final: 33 residues processed: 392 average time/residue: 0.6362 time to fit residues: 280.6209 Evaluate side-chains 400 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 362 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain T residue 589 ASP Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 316 MET Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 126 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN X 105 GLN X 203 GLN X 315 GLN Y 169 GLN Y 375 HIS Z 72 HIS Z 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101802 restraints weight = 30228.995| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.48 r_work: 0.3164 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20834 Z= 0.157 Angle : 0.570 7.711 28528 Z= 0.277 Chirality : 0.043 0.211 3546 Planarity : 0.004 0.081 3375 Dihedral : 4.210 28.539 2514 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 2.76 % Allowed : 12.69 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.88 (0.18), residues: 2316 helix: 2.40 (0.28), residues: 369 sheet: 0.92 (0.19), residues: 708 loop : -0.14 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 166 TYR 0.016 0.001 TYR E 91 PHE 0.013 0.001 PHE X 53 TRP 0.017 0.001 TRP C 32 HIS 0.007 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (20664) covalent geometry : angle 0.53566 / 0.27 (28056) SS BOND : bond 0.00355 / 0.21 ( 38) SS BOND : angle 1.35733 / 1.02 ( 76) hydrogen bonds : bond 0.04359 / 2.88 ( 570) hydrogen bonds : angle 4.40685 / 3.07 ( 1533) link_ALPHA1-2 : bond 0.00329 / 0.20 ( 12) link_ALPHA1-2 : angle 1.58155 / 1.14 ( 36) link_ALPHA1-3 : bond 0.00501 / 0.24 ( 9) link_ALPHA1-3 : angle 1.40490 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00149 / 0.07 ( 9) link_ALPHA1-6 : angle 1.62503 / 1.07 ( 27) link_BETA1-4 : bond 0.00422 / 0.31 ( 41) link_BETA1-4 : angle 1.43723 / 0.97 ( 123) link_NAG-ASN : bond 0.00266 / 0.19 ( 61) link_NAG-ASN : angle 1.82988 / 1.29 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 0.836 Fit side-chains REVERT: A 43 GLN cc_start: 0.7148 (mp10) cc_final: 0.5640 (mp10) REVERT: A 74 THR cc_start: 0.8270 (t) cc_final: 0.8044 (t) REVERT: A 100 THR cc_start: 0.8668 (m) cc_final: 0.8348 (t) REVERT: A 125 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8281 (p) REVERT: E 48 ILE cc_start: 0.8138 (mm) cc_final: 0.7935 (mp) REVERT: E 100 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: H 67 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7954 (tp) REVERT: R 624 ASN cc_start: 0.8349 (m110) cc_final: 0.8012 (m-40) REVERT: S 626 MET cc_start: 0.8407 (mtp) cc_final: 0.8122 (mtm) REVERT: X 208 ILE cc_start: 0.8252 (mm) cc_final: 0.8034 (OUTLIER) REVERT: X 211 ASP cc_start: 0.7810 (t0) cc_final: 0.7511 (t0) REVERT: X 457 ASP cc_start: 0.8034 (t0) cc_final: 0.7754 (t0) REVERT: Y 111 LEU cc_start: 0.8358 (tt) cc_final: 0.8104 (tp) REVERT: Y 207 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7542 (mtmm) REVERT: Y 347 GLU cc_start: 0.8162 (tp30) cc_final: 0.7762 (tp30) REVERT: Y 426 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5685 (mtp) REVERT: Y 456 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7466 (ttm170) REVERT: Z 105 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7741 (tp40) REVERT: Z 107 ASP cc_start: 0.8261 (m-30) cc_final: 0.7996 (t0) REVERT: Z 211 ASP cc_start: 0.7887 (t0) cc_final: 0.7635 (t0) REVERT: Z 381 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7669 (mm-30) REVERT: Z 426 MET cc_start: 0.6511 (mtt) cc_final: 0.5884 (mtt) outliers start: 57 outliers final: 37 residues processed: 386 average time/residue: 0.6540 time to fit residues: 283.8657 Evaluate side-chains 406 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 364 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 290 LYS Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 70 optimal weight: 6.9990 chunk 44 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 43 GLN L 38 GLN Y 375 HIS Z 169 GLN Z 375 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102403 restraints weight = 30184.058| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.46 r_work: 0.3169 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20834 Z= 0.134 Angle : 0.555 7.326 28528 Z= 0.270 Chirality : 0.042 0.270 3546 Planarity : 0.004 0.083 3375 Dihedral : 4.202 32.546 2514 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 3.10 % Allowed : 13.32 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2316 helix: 2.45 (0.28), residues: 369 sheet: 0.87 (0.19), residues: 741 loop : -0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Z 166 TYR 0.014 0.001 TYR E 91 PHE 0.011 0.001 PHE X 53 TRP 0.020 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (20664) covalent geometry : angle 0.52053 / 0.26 (28056) SS BOND : bond 0.00352 / 0.20 ( 38) SS BOND : angle 1.30606 / 1.01 ( 76) hydrogen bonds : bond 0.04132 / 2.74 ( 570) hydrogen bonds : angle 4.35698 / 3.04 ( 1533) link_ALPHA1-2 : bond 0.00349 / 0.21 ( 12) link_ALPHA1-2 : angle 1.54685 / 1.12 ( 36) link_ALPHA1-3 : bond 0.00501 / 0.24 ( 9) link_ALPHA1-3 : angle 1.38193 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00166 / 0.08 ( 9) link_ALPHA1-6 : angle 1.60951 / 1.06 ( 27) link_BETA1-4 : bond 0.00417 / 0.31 ( 41) link_BETA1-4 : angle 1.39956 / 0.95 ( 123) link_NAG-ASN : bond 0.00203 / 0.15 ( 61) link_NAG-ASN : angle 1.80572 / 1.26 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 377 time to evaluate : 0.773 Fit side-chains REVERT: A 43 GLN cc_start: 0.7194 (mp10) cc_final: 0.5650 (mp10) REVERT: A 74 THR cc_start: 0.8270 (t) cc_final: 0.8043 (t) REVERT: A 100 THR cc_start: 0.8635 (m) cc_final: 0.8314 (t) REVERT: A 125 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8306 (p) REVERT: D 116 MET cc_start: 0.8573 (mtp) cc_final: 0.8335 (mtp) REVERT: E 48 ILE cc_start: 0.8149 (mm) cc_final: 0.7935 (mp) REVERT: E 100 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: H 67 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7964 (tp) REVERT: L 104 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7658 (p) REVERT: R 624 ASN cc_start: 0.8336 (m110) cc_final: 0.7983 (m-40) REVERT: S 626 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: X 203 GLN cc_start: 0.8601 (tt0) cc_final: 0.8400 (tt0) REVERT: X 208 ILE cc_start: 0.8275 (mm) cc_final: 0.8057 (OUTLIER) REVERT: X 211 ASP cc_start: 0.7806 (t0) cc_final: 0.7522 (t0) REVERT: X 389 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8296 (ptmt) REVERT: X 457 ASP cc_start: 0.7994 (t0) cc_final: 0.7723 (t0) REVERT: Y 111 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (tp) REVERT: Y 207 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7438 (mtmm) REVERT: Y 347 GLU cc_start: 0.8177 (tp30) cc_final: 0.7800 (tp30) REVERT: Y 422 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: Y 426 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5675 (mtp) REVERT: Y 456 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7498 (ttm170) REVERT: Y 503 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7206 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: Z 107 ASP cc_start: 0.8246 (m-30) cc_final: 0.7953 (t0) REVERT: Z 211 ASP cc_start: 0.7892 (t0) cc_final: 0.7639 (t0) REVERT: Z 326 ILE cc_start: 0.8462 (pt) cc_final: 0.8022 (mm) REVERT: Z 381 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7722 (mm-30) REVERT: Z 426 MET cc_start: 0.6467 (mtt) cc_final: 0.5839 (mtt) REVERT: Z 475 ILE cc_start: 0.8339 (tp) cc_final: 0.8102 (tp) outliers start: 64 outliers final: 41 residues processed: 397 average time/residue: 0.6476 time to fit residues: 288.5198 Evaluate side-chains 416 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 626 MET Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 290 LYS Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 222 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN X 315 GLN Y 375 HIS Z 169 GLN Z 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101626 restraints weight = 30272.780| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.46 r_work: 0.3161 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20834 Z= 0.170 Angle : 0.584 7.667 28528 Z= 0.284 Chirality : 0.043 0.172 3546 Planarity : 0.004 0.080 3375 Dihedral : 4.266 31.808 2514 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 3.25 % Allowed : 13.76 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2316 helix: 2.41 (0.28), residues: 369 sheet: 0.88 (0.19), residues: 738 loop : -0.14 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 166 TYR 0.016 0.001 TYR E 91 PHE 0.013 0.001 PHE X 53 TRP 0.020 0.001 TRP C 32 HIS 0.008 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (20664) covalent geometry : angle 0.54800 / 0.28 (28056) SS BOND : bond 0.00400 / 0.23 ( 38) SS BOND : angle 1.45533 / 1.12 ( 76) hydrogen bonds : bond 0.04471 / 2.96 ( 570) hydrogen bonds : angle 4.40960 / 3.08 ( 1533) link_ALPHA1-2 : bond 0.00312 / 0.19 ( 12) link_ALPHA1-2 : angle 1.61998 / 1.17 ( 36) link_ALPHA1-3 : bond 0.00461 / 0.22 ( 9) link_ALPHA1-3 : angle 1.41484 / 0.99 ( 27) link_ALPHA1-6 : bond 0.00144 / 0.07 ( 9) link_ALPHA1-6 : angle 1.63052 / 1.08 ( 27) link_BETA1-4 : bond 0.00418 / 0.31 ( 41) link_BETA1-4 : angle 1.48047 / 1.00 ( 123) link_NAG-ASN : bond 0.00281 / 0.20 ( 61) link_NAG-ASN : angle 1.88031 / 1.32 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 370 time to evaluate : 0.751 Fit side-chains REVERT: A 74 THR cc_start: 0.8271 (t) cc_final: 0.8047 (t) REVERT: A 100 THR cc_start: 0.8705 (m) cc_final: 0.8386 (t) REVERT: A 125 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8326 (p) REVERT: D 55 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7904 (mmtt) REVERT: D 116 MET cc_start: 0.8539 (mtp) cc_final: 0.8321 (mtp) REVERT: E 100 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6636 (pm20) REVERT: H 67 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8001 (tp) REVERT: R 610 TRP cc_start: 0.8547 (t-100) cc_final: 0.8091 (t-100) REVERT: R 624 ASN cc_start: 0.8369 (m110) cc_final: 0.7977 (m-40) REVERT: R 661 LEU cc_start: 0.8327 (mt) cc_final: 0.8094 (mp) REVERT: S 626 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: T 601 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8576 (mtpp) REVERT: X 211 ASP cc_start: 0.7817 (t0) cc_final: 0.7539 (t0) REVERT: X 389 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8297 (ptmt) REVERT: X 457 ASP cc_start: 0.8012 (t0) cc_final: 0.7725 (t0) REVERT: Y 111 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (tp) REVERT: Y 164 GLU cc_start: 0.7752 (pm20) cc_final: 0.7399 (pm20) REVERT: Y 207 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7503 (mtmm) REVERT: Y 347 GLU cc_start: 0.8194 (tp30) cc_final: 0.7824 (tp30) REVERT: Y 422 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: Y 426 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5801 (mtp) REVERT: Y 456 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: Y 503 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7153 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: Z 107 ASP cc_start: 0.8281 (m-30) cc_final: 0.7985 (t0) REVERT: Z 211 ASP cc_start: 0.7893 (t0) cc_final: 0.7625 (t0) REVERT: Z 326 ILE cc_start: 0.8524 (pt) cc_final: 0.8101 (mm) REVERT: Z 381 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7803 (mm-30) REVERT: Z 426 MET cc_start: 0.6529 (mtt) cc_final: 0.5935 (mtt) REVERT: Z 475 ILE cc_start: 0.8366 (tp) cc_final: 0.8118 (tp) outliers start: 67 outliers final: 45 residues processed: 394 average time/residue: 0.6324 time to fit residues: 280.0752 Evaluate side-chains 423 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 576 LEU Chi-restraints excluded: chain S residue 626 MET Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 601 LYS Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 305 THR Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 290 LYS Chi-restraints excluded: chain Y residue 422 GLN Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 443 ILE Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 268 GLU Chi-restraints excluded: chain Z residue 303 THR Chi-restraints excluded: chain Z residue 464 THR Chi-restraints excluded: chain Z residue 490 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 85 optimal weight: 0.0870 chunk 113 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 183 optimal weight: 0.0980 chunk 138 optimal weight: 0.0000 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 165 optimal weight: 0.5980 overall best weight: 0.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Y 169 GLN Y 375 HIS Z 169 GLN Z 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104146 restraints weight = 30143.009| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.47 r_work: 0.3200 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20834 Z= 0.088 Angle : 0.520 7.663 28528 Z= 0.255 Chirality : 0.041 0.152 3546 Planarity : 0.004 0.079 3375 Dihedral : 4.020 27.578 2514 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 14.87 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.96 (0.18), residues: 2316 helix: 2.58 (0.28), residues: 369 sheet: 0.80 (0.19), residues: 768 loop : -0.05 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 166 TYR 0.010 0.001 TYR E 91 PHE 0.011 0.001 PHE X 53 TRP 0.026 0.001 TRP L 32 HIS 0.009 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (20664) covalent geometry : angle 0.49406 / 0.25 (28056) SS BOND : bond 0.00349 / 0.17 ( 38) SS BOND : angle 1.11406 / 0.88 ( 76) hydrogen bonds : bond 0.03404 / 2.26 ( 570) hydrogen bonds : angle 4.22716 / 2.94 ( 1533) link_ALPHA1-2 : bond 0.00425 / 0.26 ( 12) link_ALPHA1-2 : angle 1.43084 / 1.03 ( 36) link_ALPHA1-3 : bond 0.00560 / 0.27 ( 9) link_ALPHA1-3 : angle 1.29511 / 0.88 ( 27) link_ALPHA1-6 : bond 0.00274 / 0.13 ( 9) link_ALPHA1-6 : angle 1.49989 / 1.00 ( 27) link_BETA1-4 : bond 0.00442 / 0.32 ( 41) link_BETA1-4 : angle 1.25937 / 0.85 ( 123) link_NAG-ASN : bond 0.00184 / 0.13 ( 61) link_NAG-ASN : angle 1.49610 / 1.05 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 385 time to evaluate : 0.867 Fit side-chains REVERT: A 43 GLN cc_start: 0.7132 (mp10) cc_final: 0.5805 (mp10) REVERT: A 74 THR cc_start: 0.8268 (t) cc_final: 0.8055 (t) REVERT: A 100 THR cc_start: 0.8574 (m) cc_final: 0.8268 (t) REVERT: C 97 THR cc_start: 0.8453 (m) cc_final: 0.8053 (p) REVERT: D 67 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7919 (tp) REVERT: D 116 MET cc_start: 0.8508 (mtp) cc_final: 0.8306 (mtp) REVERT: E 92 ASP cc_start: 0.8004 (t0) cc_final: 0.7792 (t0) REVERT: E 100 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: R 624 ASN cc_start: 0.8350 (m110) cc_final: 0.7985 (m-40) REVERT: S 626 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8107 (mtm) REVERT: X 211 ASP cc_start: 0.7795 (t0) cc_final: 0.7525 (t0) REVERT: X 265 LEU cc_start: 0.8720 (mt) cc_final: 0.8401 (mp) REVERT: X 389 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8298 (ptmt) REVERT: X 457 ASP cc_start: 0.7953 (t0) cc_final: 0.7704 (t0) REVERT: Y 111 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8084 (tp) REVERT: Y 164 GLU cc_start: 0.7719 (pm20) cc_final: 0.7361 (pm20) REVERT: Y 207 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7448 (mtmm) REVERT: Y 308 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8241 (ttp80) REVERT: Y 347 GLU cc_start: 0.8178 (tp30) cc_final: 0.7787 (tp30) REVERT: Y 426 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5743 (mtp) REVERT: Y 456 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7492 (ttm170) REVERT: Y 503 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: Z 103 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: Z 105 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7745 (tp40) REVERT: Z 107 ASP cc_start: 0.8292 (m-30) cc_final: 0.7981 (t0) REVERT: Z 161 MET cc_start: 0.8244 (mmm) cc_final: 0.8026 (mmm) REVERT: Z 211 ASP cc_start: 0.7896 (t0) cc_final: 0.7644 (t0) REVERT: Z 230 ASP cc_start: 0.8025 (t0) cc_final: 0.7573 (t0) REVERT: Z 321 ASP cc_start: 0.8022 (t0) cc_final: 0.7766 (t0) REVERT: Z 325 ASP cc_start: 0.8021 (t0) cc_final: 0.7694 (t0) REVERT: Z 326 ILE cc_start: 0.8498 (pt) cc_final: 0.8053 (mm) REVERT: Z 381 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7763 (mm-30) REVERT: Z 426 MET cc_start: 0.6275 (mtt) cc_final: 0.5746 (mtt) REVERT: Z 475 ILE cc_start: 0.8337 (tp) cc_final: 0.8082 (tp) outliers start: 52 outliers final: 22 residues processed: 403 average time/residue: 0.6137 time to fit residues: 277.9614 Evaluate side-chains 404 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 636 SER Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 626 MET Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain T residue 592 PHE Chi-restraints excluded: chain T residue 660 LEU Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 308 ARG Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 208 ILE Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 316 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 154 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 577 GLN X 105 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100227 restraints weight = 30103.146| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.46 r_work: 0.3144 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20834 Z= 0.257 Angle : 0.668 8.520 28528 Z= 0.322 Chirality : 0.046 0.260 3546 Planarity : 0.005 0.078 3375 Dihedral : 4.438 34.425 2514 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 2.33 % Allowed : 15.55 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2316 helix: 2.29 (0.28), residues: 369 sheet: 0.83 (0.19), residues: 738 loop : -0.17 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Z 166 TYR 0.019 0.002 TYR E 91 PHE 0.017 0.002 PHE X 53 TRP 0.033 0.002 TRP L 32 HIS 0.008 0.001 HIS Y 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 (20664) covalent geometry : angle 0.62665 / 0.31 (28056) SS BOND : bond 0.00476 / 0.28 ( 38) SS BOND : angle 1.95406 / 1.49 ( 76) hydrogen bonds : bond 0.05111 / 3.39 ( 570) hydrogen bonds : angle 4.53392 / 3.17 ( 1533) link_ALPHA1-2 : bond 0.00284 / 0.18 ( 12) link_ALPHA1-2 : angle 1.76419 / 1.27 ( 36) link_ALPHA1-3 : bond 0.00411 / 0.20 ( 9) link_ALPHA1-3 : angle 1.53491 / 1.09 ( 27) link_ALPHA1-6 : bond 0.00207 / 0.10 ( 9) link_ALPHA1-6 : angle 1.72258 / 1.14 ( 27) link_BETA1-4 : bond 0.00450 / 0.33 ( 41) link_BETA1-4 : angle 1.63466 / 1.10 ( 123) link_NAG-ASN : bond 0.00464 / 0.32 ( 61) link_NAG-ASN : angle 2.12086 / 1.49 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 0.743 Fit side-chains REVERT: A 74 THR cc_start: 0.8263 (t) cc_final: 0.8049 (t) REVERT: A 100 THR cc_start: 0.8719 (m) cc_final: 0.8416 (t) REVERT: D 55 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7926 (mmtt) REVERT: E 100 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: H 67 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8010 (tp) REVERT: R 610 TRP cc_start: 0.8548 (t-100) cc_final: 0.8082 (t-100) REVERT: R 624 ASN cc_start: 0.8399 (m110) cc_final: 0.7990 (m-40) REVERT: X 211 ASP cc_start: 0.7866 (t0) cc_final: 0.7571 (t0) REVERT: X 231 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: X 389 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8308 (ptmt) REVERT: X 457 ASP cc_start: 0.8032 (t0) cc_final: 0.7756 (t0) REVERT: Y 111 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8120 (tp) REVERT: Y 207 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7589 (mtmm) REVERT: Y 347 GLU cc_start: 0.8127 (tp30) cc_final: 0.7753 (tp30) REVERT: Y 426 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.5848 (mtp) REVERT: Y 456 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7537 (ttm170) REVERT: Y 502 LYS cc_start: 0.8080 (tttp) cc_final: 0.7872 (tttp) REVERT: Y 503 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7348 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7776 (tp40) REVERT: Z 107 ASP cc_start: 0.8202 (m-30) cc_final: 0.7911 (t0) REVERT: Z 240 LYS cc_start: 0.8136 (mppt) cc_final: 0.7868 (mtmm) REVERT: Z 321 ASP cc_start: 0.8054 (t0) cc_final: 0.7816 (t0) REVERT: Z 326 ILE cc_start: 0.8546 (pt) cc_final: 0.8079 (mm) REVERT: Z 327 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: Z 349 LEU cc_start: 0.8421 (mt) cc_final: 0.8168 (mp) REVERT: Z 381 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7810 (mm-30) REVERT: Z 426 MET cc_start: 0.6595 (mtt) cc_final: 0.6020 (mtt) REVERT: Z 475 ILE cc_start: 0.8392 (tp) cc_final: 0.8141 (tp) outliers start: 48 outliers final: 30 residues processed: 398 average time/residue: 0.6836 time to fit residues: 304.6726 Evaluate side-chains 413 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 375 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain X residue 231 LYS Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 316 MET Chi-restraints excluded: chain Y residue 390 LEU Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 244 THR Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 377 ASN Chi-restraints excluded: chain Z residue 490 GLN Chi-restraints excluded: chain Z residue 502 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 191 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 224 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 190 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 43 GLN T 577 GLN X 203 GLN X 283 ASN Y 169 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 169 GLN Z 315 GLN Z 343 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102276 restraints weight = 29998.847| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.47 r_work: 0.3171 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20834 Z= 0.121 Angle : 0.570 8.440 28528 Z= 0.278 Chirality : 0.042 0.191 3546 Planarity : 0.004 0.081 3375 Dihedral : 4.230 30.854 2514 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 1.99 % Allowed : 16.42 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2316 helix: 2.38 (0.28), residues: 369 sheet: 0.84 (0.19), residues: 744 loop : -0.11 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 166 TYR 0.015 0.001 TYR E 91 PHE 0.016 0.001 PHE X 53 TRP 0.035 0.001 TRP L 32 HIS 0.010 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20664) covalent geometry : angle 0.53729 / 0.27 (28056) SS BOND : bond 0.00364 / 0.20 ( 38) SS BOND : angle 1.57563 / 1.21 ( 76) hydrogen bonds : bond 0.03991 / 2.64 ( 570) hydrogen bonds : angle 4.36609 / 3.05 ( 1533) link_ALPHA1-2 : bond 0.00380 / 0.23 ( 12) link_ALPHA1-2 : angle 1.50192 / 1.09 ( 36) link_ALPHA1-3 : bond 0.00525 / 0.25 ( 9) link_ALPHA1-3 : angle 1.35965 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00175 / 0.08 ( 9) link_ALPHA1-6 : angle 1.58764 / 1.05 ( 27) link_BETA1-4 : bond 0.00416 / 0.31 ( 41) link_BETA1-4 : angle 1.37818 / 0.93 ( 123) link_NAG-ASN : bond 0.00167 / 0.12 ( 61) link_NAG-ASN : angle 1.72856 / 1.22 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 381 time to evaluate : 0.735 Fit side-chains REVERT: A 74 THR cc_start: 0.8257 (t) cc_final: 0.8037 (t) REVERT: A 100 THR cc_start: 0.8656 (m) cc_final: 0.8337 (t) REVERT: D 55 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7886 (mmtt) REVERT: E 100 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: H 67 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8005 (tp) REVERT: R 610 TRP cc_start: 0.8553 (t-100) cc_final: 0.8087 (t-100) REVERT: R 624 ASN cc_start: 0.8349 (m110) cc_final: 0.7939 (m-40) REVERT: X 211 ASP cc_start: 0.7828 (t0) cc_final: 0.7529 (t0) REVERT: X 308 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8453 (ttp-110) REVERT: X 389 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8216 (ptmt) REVERT: X 457 ASP cc_start: 0.7979 (t0) cc_final: 0.7727 (t0) REVERT: Y 111 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8108 (tp) REVERT: Y 207 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7495 (mtmm) REVERT: Y 264 SER cc_start: 0.8560 (m) cc_final: 0.8310 (p) REVERT: Y 347 GLU cc_start: 0.8120 (tp30) cc_final: 0.7746 (tp30) REVERT: Y 426 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.5777 (mtp) REVERT: Y 427 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.7497 (m100) REVERT: Y 456 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7497 (ttm170) REVERT: Y 502 LYS cc_start: 0.7962 (tttp) cc_final: 0.7741 (tttp) REVERT: Y 503 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7447 (mtm-85) REVERT: Z 105 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7770 (tp40) REVERT: Z 107 ASP cc_start: 0.8278 (m-30) cc_final: 0.7959 (t0) REVERT: Z 161 MET cc_start: 0.8228 (mmm) cc_final: 0.7952 (mmm) REVERT: Z 321 ASP cc_start: 0.8030 (t0) cc_final: 0.7773 (t0) REVERT: Z 326 ILE cc_start: 0.8518 (pt) cc_final: 0.8061 (mm) REVERT: Z 327 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: Z 381 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7772 (mm-30) REVERT: Z 426 MET cc_start: 0.6311 (mtt) cc_final: 0.5819 (mtt) REVERT: Z 475 ILE cc_start: 0.8374 (tp) cc_final: 0.8115 (tp) outliers start: 41 outliers final: 23 residues processed: 395 average time/residue: 0.6531 time to fit residues: 289.5079 Evaluate side-chains 412 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 380 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain R residue 592 PHE Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain S residue 636 SER Chi-restraints excluded: chain X residue 246 GLN Chi-restraints excluded: chain X residue 247 CYS Chi-restraints excluded: chain X residue 308 ARG Chi-restraints excluded: chain X residue 443 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 316 MET Chi-restraints excluded: chain Y residue 426 MET Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 456 ARG Chi-restraints excluded: chain Y residue 501 CYS Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 105 GLN Chi-restraints excluded: chain Z residue 247 CYS Chi-restraints excluded: chain Z residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 43 GLN T 577 GLN ** Y 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 375 HIS Z 169 GLN Z 315 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102353 restraints weight = 30051.558| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.45 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20834 Z= 0.130 Angle : 0.572 8.711 28528 Z= 0.278 Chirality : 0.042 0.249 3546 Planarity : 0.004 0.078 3375 Dihedral : 4.179 30.208 2514 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 1.89 % Allowed : 16.72 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2316 helix: 2.42 (0.28), residues: 369 sheet: 0.75 (0.19), residues: 762 loop : -0.11 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Z 166 TYR 0.014 0.001 TYR E 91 PHE 0.016 0.001 PHE X 53 TRP 0.036 0.001 TRP L 32 HIS 0.010 0.001 HIS Y 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (20664) covalent geometry : angle 0.53871 / 0.27 (28056) SS BOND : bond 0.00364 / 0.20 ( 38) SS BOND : angle 1.53824 / 1.19 ( 76) hydrogen bonds : bond 0.03993 / 2.64 ( 570) hydrogen bonds : angle 4.31661 / 3.01 ( 1533) link_ALPHA1-2 : bond 0.00356 / 0.21 ( 12) link_ALPHA1-2 : angle 1.53601 / 1.11 ( 36) link_ALPHA1-3 : bond 0.00499 / 0.24 ( 9) link_ALPHA1-3 : angle 1.36944 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00177 / 0.08 ( 9) link_ALPHA1-6 : angle 1.59776 / 1.06 ( 27) link_BETA1-4 : bond 0.00419 / 0.31 ( 41) link_BETA1-4 : angle 1.40803 / 0.95 ( 123) link_NAG-ASN : bond 0.00205 / 0.15 ( 61) link_NAG-ASN : angle 1.75512 / 1.23 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7587.83 seconds wall clock time: 130 minutes 3.63 seconds (7803.63 seconds total)