Starting phenix.real_space_refine on Sun Sep 13 03:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dfh_7876/09_2026/6dfh_7876.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 120 5.16 5 C 12618 2.51 5 N 3288 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20046 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "D" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 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: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" 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: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 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 Time building chain proxies: 4.65, per 1000 atoms: 0.23 Number of scatterers: 20046 At special positions: 0 Unit cell: (152.44, 156.56, 143.17, 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 120 16.00 O 4020 8.00 N 3288 7.00 C 12618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.01 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=1.99 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 R 4 " - " MAN R 5 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN Z 4 " - " MAN Z 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN h 4 " - " MAN h 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " BMA a 3 " - " MAN a 7 " " BMA i 3 " - " MAN i 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 603 " - " ASN A 160 " " NAG A 608 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 626 " - " ASN A 339 " " NAG A 627 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 603 " - " ASN C 160 " " NAG C 608 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 626 " - " ASN C 339 " " NAG C 627 " - " ASN C 392 " " NAG D 603 " - " ASN D 160 " " NAG D 608 " - " ASN D 301 " " NAG D 611 " - " ASN D 197 " " NAG D 626 " - " ASN D 339 " " NAG D 627 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 448 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 295 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 332 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN D 156 " " NAG d 1 " - " ASN D 276 " " NAG e 1 " - " ASN D 295 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 234 " " NAG h 1 " - " ASN D 262 " " NAG i 1 " - " ASN D 332 " " NAG j 1 " - " ASN D 448 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 829.5 milliseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 54 sheets defined 19.2% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.950A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.726A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.763A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.924A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.592A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.763A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.736A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.951A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.727A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.762A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.925A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 535 removed outlier: 3.593A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 532 through 535' Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.763A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 584 " --> pdb=" O VAL E 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP E 589 " --> pdb=" O HIS E 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 590 " --> pdb=" O TYR E 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY E 594 " --> pdb=" O GLN E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 625 Processing helix chain 'E' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.735A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.951A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.727A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.763A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.925A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 removed outlier: 3.593A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.764A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.736A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.559A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N LYS A 487 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP A 47 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL A 489 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TRP A 45 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ILE A 491 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU A 260 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU A 260 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.332A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.908A pdb=" N ASN A 301 " --> pdb=" O LEU A 323A" (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS A 305 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 72 Processing sheet with id=AB6, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 24 removed outlier: 3.762A pdb=" N CYS L 23 " --> pdb=" O VAL L 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.376A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.558A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LYS C 487 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP C 47 " --> pdb=" O LYS C 487 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL C 489 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP C 45 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ILE C 491 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.560A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU C 260 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU C 260 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 377 removed outlier: 4.331A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.909A pdb=" N ASN C 301 " --> pdb=" O LEU C 323A" (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS C 305 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 67 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AD8, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.762A pdb=" N CYS J 23 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.375A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.559A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LYS D 487 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 47 " --> pdb=" O LYS D 487 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL D 489 " --> pdb=" O TRP D 45 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP D 45 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ILE D 491 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.561A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 173 through 177 Processing sheet with id=AE5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AE6, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU D 260 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU D 260 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 374 through 377 removed outlier: 4.331A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 301 through 308 removed outlier: 3.908A pdb=" N ASN D 301 " --> pdb=" O LEU D 323A" (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D 305 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 67 through 72 Processing sheet with id=AF6, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AF7, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AF8, first strand: chain 'K' and resid 18 through 24 removed outlier: 3.763A pdb=" N CYS K 23 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.375A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1539 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: 4.08 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 - 1.34: 6187 1.34 - 1.46: 4939 1.46 - 1.58: 9178 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 20466 Sorted by residual: bond pdb=" C5 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.418 1.466 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C5 MAN h 4 " pdb=" O5 MAN h 4 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C1 NAG D 608 " pdb=" O5 NAG D 608 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.91e+00 ... (remaining 20461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 26450 2.19 - 4.39: 1174 4.39 - 6.58: 123 6.58 - 8.77: 54 8.77 - 10.97: 15 Bond angle restraints: 27816 Sorted by residual: angle pdb=" C GLU A 64 " pdb=" N LYS A 65 " pdb=" CA LYS A 65 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLU D 64 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C GLU C 64 " pdb=" N LYS C 65 " pdb=" CA LYS C 65 " ideal model delta sigma weight residual 121.54 132.42 -10.88 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C GLU C 87 " pdb=" N ASN C 88 " pdb=" CA ASN C 88 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 angle pdb=" C GLU D 87 " pdb=" N ASN D 88 " pdb=" CA ASN D 88 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 ... (remaining 27811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 10847 15.21 - 30.43: 502 30.43 - 45.64: 177 45.64 - 60.85: 15 60.85 - 76.06: 21 Dihedral angle restraints: 11562 sinusoidal: 4626 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -162.06 76.06 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -161.94 75.94 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS D 501 " pdb=" SG CYS D 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 11559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2579 0.068 - 0.135: 720 0.135 - 0.203: 78 0.203 - 0.270: 6 0.270 - 0.338: 10 Chirality restraints: 3393 Sorted by residual: chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C5 BMA i 3 " pdb=" C4 BMA i 3 " pdb=" C6 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 3390 not shown) Planarity restraints: 3435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 65 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C LYS D 65 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS D 65 " -0.020 2.00e-02 2.50e+03 pdb=" N HIS D 66 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 65 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C LYS A 65 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS A 65 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS A 66 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 65 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C LYS C 65 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS C 65 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS C 66 " 0.017 2.00e-02 2.50e+03 ... (remaining 3432 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4696 2.78 - 3.31: 17698 3.31 - 3.84: 33530 3.84 - 4.37: 36996 4.37 - 4.90: 61133 Nonbonded interactions: 154053 Sorted by model distance: nonbonded pdb=" OE2 GLU D 64 " pdb=" O4 MAN h 4 " model vdw 2.252 3.040 nonbonded pdb=" O THR D 278 " pdb=" O6 NAG d 1 " model vdw 2.257 3.040 nonbonded pdb=" O ASN D 478 " pdb=" OG SER D 481 " model vdw 2.282 3.040 nonbonded pdb=" O ASN C 478 " pdb=" OG SER C 481 " model vdw 2.282 3.040 nonbonded pdb=" O ASN A 478 " pdb=" OG SER A 481 " model vdw 2.283 3.040 ... (remaining 154048 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'Z' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.010 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.009 0.103 20595 Z= 0.413 Angle : 1.097 12.122 28164 Z= 0.537 Chirality : 0.060 0.338 3393 Planarity : 0.007 0.067 3393 Dihedral : 10.083 75.313 6987 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.28 % Allowed : 1.85 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.15), residues: 2358 helix: -3.26 (0.18), residues: 354 sheet: -2.19 (0.19), residues: 657 loop : -2.94 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 327 TYR 0.024 0.003 TYR C 217 PHE 0.023 0.004 PHE A 391 TRP 0.037 0.004 TRP B 614 HIS 0.008 0.003 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.41 (20466) covalent geometry : angle 1.04924 / 0.53 (27816) SS BOND : bond 0.01255 / 0.82 ( 39) SS BOND : angle 1.78222 / 1.27 ( 78) hydrogen bonds : bond 0.27877 / 18.55 ( 564) hydrogen bonds : angle 11.10679 / 7.55 ( 1539) link_ALPHA1-2 : bond 0.00682 / 0.37 ( 9) link_ALPHA1-2 : angle 2.28733 / 1.42 ( 27) link_ALPHA1-3 : bond 0.00333 / 0.16 ( 6) link_ALPHA1-3 : angle 1.98851 / 1.13 ( 18) link_ALPHA1-6 : bond 0.00117 / 0.06 ( 3) link_ALPHA1-6 : angle 2.53479 / 1.78 ( 9) link_BETA1-4 : bond 0.00527 / 0.30 ( 30) link_BETA1-4 : angle 3.11673 / 2.13 ( 90) link_NAG-ASN : bond 0.01383 / 0.79 ( 42) link_NAG-ASN : angle 3.83121 / 2.78 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 274 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.9367 (t) cc_final: 0.8977 (t) REVERT: A 110 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 116 LEU cc_start: 0.9669 (tp) cc_final: 0.9433 (tt) REVERT: A 150 MET cc_start: 0.9446 (mmm) cc_final: 0.8123 (mpp) REVERT: A 195 ASN cc_start: 0.8631 (p0) cc_final: 0.8346 (p0) REVERT: A 328 MET cc_start: 0.8724 (tpt) cc_final: 0.8222 (tpt) REVERT: B 539 VAL cc_start: 0.9350 (t) cc_final: 0.8863 (p) REVERT: B 589 ASP cc_start: 0.9395 (p0) cc_final: 0.8843 (p0) REVERT: B 606 THR cc_start: 0.9437 (p) cc_final: 0.9103 (p) REVERT: B 612 SER cc_start: 0.9162 (p) cc_final: 0.8840 (m) REVERT: B 626 MET cc_start: 0.7987 (mtp) cc_final: 0.7216 (ttm) REVERT: B 648 GLU cc_start: 0.9674 (tt0) cc_final: 0.9132 (pp20) REVERT: B 650 GLN cc_start: 0.6744 (pt0) cc_final: 0.6079 (mp-120) REVERT: L 30 LYS cc_start: 0.9587 (mttt) cc_final: 0.9366 (mtpt) REVERT: C 36 VAL cc_start: 0.9412 (t) cc_final: 0.9119 (t) REVERT: C 150 MET cc_start: 0.9535 (mmm) cc_final: 0.9045 (mmm) REVERT: E 589 ASP cc_start: 0.9425 (p0) cc_final: 0.8685 (p0) REVERT: E 626 MET cc_start: 0.7859 (mtp) cc_final: 0.7318 (ttm) REVERT: E 638 TYR cc_start: 0.8947 (m-80) cc_final: 0.8702 (m-10) REVERT: E 648 GLU cc_start: 0.9617 (tt0) cc_final: 0.9081 (pp20) REVERT: E 654 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8768 (tm-30) REVERT: G 100 GLU cc_start: 0.8415 (tt0) cc_final: 0.8028 (tt0) REVERT: J 30 LYS cc_start: 0.9535 (mttt) cc_final: 0.9320 (mtpt) REVERT: D 36 VAL cc_start: 0.9272 (t) cc_final: 0.8875 (t) REVERT: D 150 MET cc_start: 0.9485 (mmm) cc_final: 0.8001 (mpp) REVERT: D 195 ASN cc_start: 0.8592 (p0) cc_final: 0.8371 (p0) REVERT: D 328 MET cc_start: 0.8851 (tpt) cc_final: 0.8289 (tpt) REVERT: F 589 ASP cc_start: 0.9400 (p0) cc_final: 0.8707 (p0) REVERT: F 612 SER cc_start: 0.9138 (p) cc_final: 0.8832 (m) REVERT: F 626 MET cc_start: 0.7765 (mtp) cc_final: 0.7256 (ttm) REVERT: F 638 TYR cc_start: 0.8984 (m-80) cc_final: 0.8768 (m-10) REVERT: F 648 GLU cc_start: 0.9647 (tt0) cc_final: 0.9167 (pp20) REVERT: F 654 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8817 (tm-30) REVERT: I 100 GLU cc_start: 0.8115 (tt0) cc_final: 0.7904 (tt0) REVERT: K 53 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9098 (mp0) outliers start: 6 outliers final: 0 residues processed: 280 average time/residue: 0.1953 time to fit residues: 77.9368 Evaluate side-chains 154 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS B 543 ASN B 563 GLN C 374 HIS E 563 GLN D 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.040749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031599 restraints weight = 147362.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032677 restraints weight = 79260.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033409 restraints weight = 52971.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.033927 restraints weight = 40408.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.034277 restraints weight = 33518.691| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20595 Z= 0.218 Angle : 0.788 12.407 28164 Z= 0.393 Chirality : 0.046 0.180 3393 Planarity : 0.005 0.049 3393 Dihedral : 6.208 27.366 2565 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.23 % Allowed : 6.17 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.16), residues: 2358 helix: -1.49 (0.23), residues: 402 sheet: -1.75 (0.18), residues: 723 loop : -2.50 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.014 0.001 TYR C 217 PHE 0.018 0.002 PHE D 391 TRP 0.018 0.002 TRP E 623 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (20466) covalent geometry : angle 0.76099 / 0.39 (27816) SS BOND : bond 0.00403 / 0.26 ( 39) SS BOND : angle 0.89404 / 0.60 ( 78) hydrogen bonds : bond 0.04359 / 2.90 ( 564) hydrogen bonds : angle 7.68217 / 5.25 ( 1539) link_ALPHA1-2 : bond 0.00234 / 0.13 ( 9) link_ALPHA1-2 : angle 1.82412 / 1.11 ( 27) link_ALPHA1-3 : bond 0.00173 / 0.08 ( 6) link_ALPHA1-3 : angle 1.35567 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00259 / 0.13 ( 3) link_ALPHA1-6 : angle 1.52414 / 1.04 ( 9) link_BETA1-4 : bond 0.00347 / 0.18 ( 30) link_BETA1-4 : angle 2.04997 / 1.46 ( 90) link_NAG-ASN : bond 0.00386 / 0.23 ( 42) link_NAG-ASN : angle 2.47846 / 1.71 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8458 (tm-30) REVERT: A 150 MET cc_start: 0.9505 (mmm) cc_final: 0.9039 (mpp) REVERT: B 530 MET cc_start: 0.7645 (mpp) cc_final: 0.7431 (mpp) REVERT: B 589 ASP cc_start: 0.9104 (p0) cc_final: 0.8605 (p0) REVERT: B 648 GLU cc_start: 0.9579 (tt0) cc_final: 0.9252 (tp30) REVERT: B 650 GLN cc_start: 0.7062 (pt0) cc_final: 0.6193 (mp10) REVERT: L 30 LYS cc_start: 0.9572 (mttt) cc_final: 0.9319 (mtpt) REVERT: C 100 MET cc_start: 0.9576 (mtm) cc_final: 0.9235 (mtm) REVERT: C 110 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 150 MET cc_start: 0.9394 (mmm) cc_final: 0.9172 (tpp) REVERT: C 328 MET cc_start: 0.8982 (tpt) cc_final: 0.8625 (tpt) REVERT: E 530 MET cc_start: 0.7489 (mpp) cc_final: 0.6688 (mpp) REVERT: E 589 ASP cc_start: 0.9226 (p0) cc_final: 0.8839 (p0) REVERT: E 648 GLU cc_start: 0.9492 (tt0) cc_final: 0.8874 (tp30) REVERT: E 654 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8584 (tm-30) REVERT: G 18 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8203 (mm) REVERT: G 20 LEU cc_start: 0.8901 (mp) cc_final: 0.8273 (tt) REVERT: G 46 GLU cc_start: 0.8865 (tp30) cc_final: 0.8585 (tp30) REVERT: G 100 GLU cc_start: 0.8245 (tt0) cc_final: 0.7844 (tt0) REVERT: J 30 LYS cc_start: 0.9551 (mttt) cc_final: 0.9337 (mtpt) REVERT: D 95 MET cc_start: 0.9043 (tmm) cc_final: 0.8799 (tmm) REVERT: D 150 MET cc_start: 0.9465 (mmm) cc_final: 0.9054 (mmm) REVERT: D 217 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: D 475 MET cc_start: 0.8866 (mmp) cc_final: 0.8642 (mmm) REVERT: F 589 ASP cc_start: 0.9204 (p0) cc_final: 0.8757 (p0) REVERT: F 648 GLU cc_start: 0.9481 (tt0) cc_final: 0.9031 (tp30) REVERT: F 654 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8582 (tm-30) outliers start: 26 outliers final: 5 residues processed: 209 average time/residue: 0.1665 time to fit residues: 53.2761 Evaluate side-chains 159 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 117 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 135 optimal weight: 40.0000 chunk 94 optimal weight: 0.0770 chunk 129 optimal weight: 10.0000 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 543 ASN B 652 GLN H 33 ASN C 82 GLN E 652 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN F 652 GLN ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.030202 restraints weight = 152043.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.031263 restraints weight = 81428.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031984 restraints weight = 54060.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032486 restraints weight = 41208.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032803 restraints weight = 34208.584| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20595 Z= 0.284 Angle : 0.792 10.258 28164 Z= 0.391 Chirality : 0.045 0.200 3393 Planarity : 0.004 0.042 3393 Dihedral : 5.961 28.173 2565 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.61 % Allowed : 8.17 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.17), residues: 2358 helix: -0.81 (0.25), residues: 423 sheet: -1.25 (0.19), residues: 684 loop : -2.40 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.017 0.002 TYR B 638 PHE 0.016 0.002 PHE D 391 TRP 0.017 0.002 TRP H 36 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (20466) covalent geometry : angle 0.76619 / 0.39 (27816) SS BOND : bond 0.00883 / 0.69 ( 39) SS BOND : angle 1.23724 / 0.93 ( 78) hydrogen bonds : bond 0.04143 / 2.80 ( 564) hydrogen bonds : angle 7.13277 / 4.90 ( 1539) link_ALPHA1-2 : bond 0.00399 / 0.22 ( 9) link_ALPHA1-2 : angle 2.02724 / 1.25 ( 27) link_ALPHA1-3 : bond 0.00068 / 0.04 ( 6) link_ALPHA1-3 : angle 1.45473 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00095 / 0.05 ( 3) link_ALPHA1-6 : angle 1.58012 / 1.06 ( 9) link_BETA1-4 : bond 0.00492 / 0.27 ( 30) link_BETA1-4 : angle 2.06141 / 1.48 ( 90) link_NAG-ASN : bond 0.00600 / 0.36 ( 42) link_NAG-ASN : angle 2.31532 / 1.60 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8447 (tm-30) REVERT: A 150 MET cc_start: 0.9483 (mmm) cc_final: 0.8924 (mmm) REVERT: B 589 ASP cc_start: 0.9212 (p0) cc_final: 0.8948 (p0) REVERT: B 647 GLU cc_start: 0.9312 (pt0) cc_final: 0.9071 (pp20) REVERT: B 648 GLU cc_start: 0.9609 (tt0) cc_final: 0.9042 (pt0) REVERT: B 650 GLN cc_start: 0.7062 (pt0) cc_final: 0.6619 (pt0) REVERT: H 100 GLU cc_start: 0.7982 (tt0) cc_final: 0.7759 (tt0) REVERT: L 30 LYS cc_start: 0.9570 (mttt) cc_final: 0.9345 (mtpt) REVERT: C 110 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 475 MET cc_start: 0.9048 (mmm) cc_final: 0.8802 (mmm) REVERT: E 530 MET cc_start: 0.7682 (mpp) cc_final: 0.6841 (mpp) REVERT: E 589 ASP cc_start: 0.9241 (p0) cc_final: 0.8898 (p0) REVERT: E 626 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7608 (ptp) REVERT: E 648 GLU cc_start: 0.9553 (tt0) cc_final: 0.9126 (pt0) REVERT: E 654 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8610 (tm-30) REVERT: G 46 GLU cc_start: 0.8924 (tp30) cc_final: 0.8456 (tm-30) REVERT: G 100 GLU cc_start: 0.8131 (tt0) cc_final: 0.7742 (tt0) REVERT: J 30 LYS cc_start: 0.9559 (mttt) cc_final: 0.9341 (mtpt) REVERT: D 150 MET cc_start: 0.9393 (mmm) cc_final: 0.9188 (tpp) REVERT: D 217 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: F 589 ASP cc_start: 0.9178 (p0) cc_final: 0.8914 (p0) REVERT: F 626 MET cc_start: 0.7685 (ptp) cc_final: 0.7104 (ptm) REVERT: F 648 GLU cc_start: 0.9525 (tt0) cc_final: 0.9123 (pt0) REVERT: F 654 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8554 (tm-30) REVERT: I 20 LEU cc_start: 0.8872 (mp) cc_final: 0.8231 (tt) outliers start: 34 outliers final: 16 residues processed: 188 average time/residue: 0.1596 time to fit residues: 45.6637 Evaluate side-chains 168 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 92 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN B 543 ASN C 478 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN F 543 ASN I 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.029426 restraints weight = 154414.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.030450 restraints weight = 83965.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.031154 restraints weight = 56154.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031633 restraints weight = 42886.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031958 restraints weight = 35752.871| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 20595 Z= 0.367 Angle : 0.864 11.392 28164 Z= 0.422 Chirality : 0.047 0.188 3393 Planarity : 0.005 0.045 3393 Dihedral : 6.005 27.895 2565 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.47 % Allowed : 9.35 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.17), residues: 2358 helix: -0.53 (0.26), residues: 405 sheet: -1.14 (0.19), residues: 675 loop : -2.49 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 327 TYR 0.018 0.002 TYR D 217 PHE 0.017 0.002 PHE D 391 TRP 0.017 0.002 TRP H 35 HIS 0.007 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.37 (20466) covalent geometry : angle 0.83734 / 0.42 (27816) SS BOND : bond 0.00550 / 0.36 ( 39) SS BOND : angle 1.07966 / 0.73 ( 78) hydrogen bonds : bond 0.03961 / 2.68 ( 564) hydrogen bonds : angle 6.91032 / 4.76 ( 1539) link_ALPHA1-2 : bond 0.00679 / 0.38 ( 9) link_ALPHA1-2 : angle 2.28593 / 1.42 ( 27) link_ALPHA1-3 : bond 0.00211 / 0.12 ( 6) link_ALPHA1-3 : angle 1.53241 / 0.85 ( 18) link_ALPHA1-6 : bond 0.00049 / 0.03 ( 3) link_ALPHA1-6 : angle 1.55906 / 1.03 ( 9) link_BETA1-4 : bond 0.00571 / 0.31 ( 30) link_BETA1-4 : angle 2.16382 / 1.56 ( 90) link_NAG-ASN : bond 0.00836 / 0.50 ( 42) link_NAG-ASN : angle 2.54106 / 1.76 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9579 (OUTLIER) cc_final: 0.9176 (m100) REVERT: A 110 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 150 MET cc_start: 0.9370 (mmm) cc_final: 0.8991 (mmm) REVERT: A 166 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7851 (tmm-80) REVERT: A 195 ASN cc_start: 0.7933 (p0) cc_final: 0.7633 (p0) REVERT: B 589 ASP cc_start: 0.9185 (p0) cc_final: 0.8816 (p0) REVERT: B 626 MET cc_start: 0.7713 (ptp) cc_final: 0.7223 (ptp) REVERT: B 647 GLU cc_start: 0.9340 (pt0) cc_final: 0.9093 (pp20) REVERT: B 648 GLU cc_start: 0.9617 (tt0) cc_final: 0.9069 (pt0) REVERT: B 650 GLN cc_start: 0.7074 (pt0) cc_final: 0.6569 (pt0) REVERT: H 100 GLU cc_start: 0.7979 (tt0) cc_final: 0.7718 (tt0) REVERT: H 100 MET cc_start: 0.7464 (ppp) cc_final: 0.7262 (ppp) REVERT: C 69 TRP cc_start: 0.9575 (OUTLIER) cc_final: 0.8741 (m100) REVERT: C 195 ASN cc_start: 0.7798 (p0) cc_final: 0.7446 (p0) REVERT: C 475 MET cc_start: 0.9058 (mmm) cc_final: 0.8762 (mmm) REVERT: E 584 GLU cc_start: 0.8890 (pm20) cc_final: 0.8671 (pm20) REVERT: E 589 ASP cc_start: 0.9281 (p0) cc_final: 0.8990 (p0) REVERT: E 648 GLU cc_start: 0.9607 (tt0) cc_final: 0.9153 (pt0) REVERT: E 654 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8546 (tm-30) REVERT: G 46 GLU cc_start: 0.9007 (tp30) cc_final: 0.8748 (tp30) REVERT: G 100 GLU cc_start: 0.8082 (tt0) cc_final: 0.7743 (tt0) REVERT: G 100 TYR cc_start: 0.8615 (m-10) cc_final: 0.8039 (m-10) REVERT: J 30 LYS cc_start: 0.9548 (mttt) cc_final: 0.9327 (mtpt) REVERT: D 195 ASN cc_start: 0.7860 (t0) cc_final: 0.7604 (t0) REVERT: D 217 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8192 (m-10) REVERT: D 475 MET cc_start: 0.9115 (mmp) cc_final: 0.8898 (mmm) REVERT: F 589 ASP cc_start: 0.9223 (p0) cc_final: 0.8976 (p0) REVERT: F 648 GLU cc_start: 0.9521 (tt0) cc_final: 0.9132 (pt0) REVERT: F 654 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8538 (tm-30) REVERT: I 100 TYR cc_start: 0.8701 (m-10) cc_final: 0.8435 (m-10) outliers start: 52 outliers final: 26 residues processed: 190 average time/residue: 0.1508 time to fit residues: 44.5584 Evaluate side-chains 169 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 79 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 0.0370 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.039972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030897 restraints weight = 146852.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.031977 restraints weight = 78205.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032721 restraints weight = 51844.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033222 restraints weight = 39303.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.033551 restraints weight = 32590.817| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20595 Z= 0.138 Angle : 0.696 16.507 28164 Z= 0.337 Chirality : 0.044 0.192 3393 Planarity : 0.004 0.041 3393 Dihedral : 5.567 26.877 2565 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.76 % Allowed : 10.11 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.17), residues: 2358 helix: -0.30 (0.27), residues: 423 sheet: -1.02 (0.19), residues: 702 loop : -2.17 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.012 0.001 TYR A 217 PHE 0.014 0.001 PHE D 391 TRP 0.020 0.001 TRP I 36 HIS 0.003 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (20466) covalent geometry : angle 0.67423 / 0.33 (27816) SS BOND : bond 0.00340 / 0.24 ( 39) SS BOND : angle 0.85564 / 0.62 ( 78) hydrogen bonds : bond 0.03316 / 2.24 ( 564) hydrogen bonds : angle 6.49030 / 4.47 ( 1539) link_ALPHA1-2 : bond 0.00093 / 0.05 ( 9) link_ALPHA1-2 : angle 1.65066 / 1.03 ( 27) link_ALPHA1-3 : bond 0.00297 / 0.14 ( 6) link_ALPHA1-3 : angle 1.46134 / 0.82 ( 18) link_ALPHA1-6 : bond 0.00111 / 0.06 ( 3) link_ALPHA1-6 : angle 1.66854 / 1.15 ( 9) link_BETA1-4 : bond 0.00216 / 0.12 ( 30) link_BETA1-4 : angle 1.75645 / 1.25 ( 90) link_NAG-ASN : bond 0.00321 / 0.19 ( 42) link_NAG-ASN : angle 2.01283 / 1.36 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7757 (tmm-80) REVERT: B 589 ASP cc_start: 0.9177 (p0) cc_final: 0.8813 (p0) REVERT: B 626 MET cc_start: 0.7445 (ptp) cc_final: 0.6846 (ptp) REVERT: B 647 GLU cc_start: 0.9319 (pt0) cc_final: 0.9090 (pp20) REVERT: B 648 GLU cc_start: 0.9537 (tt0) cc_final: 0.9011 (pt0) REVERT: E 530 MET cc_start: 0.7996 (mpp) cc_final: 0.7596 (mpp) REVERT: E 589 ASP cc_start: 0.9218 (p0) cc_final: 0.8882 (p0) REVERT: E 648 GLU cc_start: 0.9466 (tt0) cc_final: 0.8945 (tp30) REVERT: E 654 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8514 (tm-30) REVERT: G 46 GLU cc_start: 0.8899 (tp30) cc_final: 0.8666 (tp30) REVERT: G 100 GLU cc_start: 0.8003 (tt0) cc_final: 0.7640 (tt0) REVERT: G 100 TYR cc_start: 0.8389 (m-10) cc_final: 0.8030 (m-10) REVERT: J 30 LYS cc_start: 0.9547 (mttt) cc_final: 0.9323 (mtpt) REVERT: D 65 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8126 (mmmt) REVERT: D 69 TRP cc_start: 0.9558 (OUTLIER) cc_final: 0.9298 (m100) REVERT: D 110 GLU cc_start: 0.9187 (tp30) cc_final: 0.8900 (tp30) REVERT: D 217 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8314 (m-10) REVERT: D 475 MET cc_start: 0.9009 (mmp) cc_final: 0.8766 (mmm) REVERT: F 589 ASP cc_start: 0.9132 (p0) cc_final: 0.8768 (p0) REVERT: F 626 MET cc_start: 0.7465 (ptp) cc_final: 0.7113 (ptp) REVERT: F 648 GLU cc_start: 0.9457 (tt0) cc_final: 0.9076 (pt0) REVERT: F 654 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8467 (tm-30) REVERT: I 100 TYR cc_start: 0.8506 (m-10) cc_final: 0.8226 (m-10) outliers start: 37 outliers final: 15 residues processed: 188 average time/residue: 0.1488 time to fit residues: 43.4158 Evaluate side-chains 165 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 81 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 144 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029792 restraints weight = 151421.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.030819 restraints weight = 81004.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.031537 restraints weight = 54035.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032020 restraints weight = 41288.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.032327 restraints weight = 34370.115| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 20595 Z= 0.293 Angle : 0.797 14.457 28164 Z= 0.386 Chirality : 0.045 0.190 3393 Planarity : 0.004 0.036 3393 Dihedral : 5.620 26.708 2565 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.09 % Allowed : 10.30 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 2358 helix: -0.28 (0.27), residues: 405 sheet: -0.75 (0.20), residues: 675 loop : -2.34 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 94 TYR 0.015 0.002 TYR D 217 PHE 0.014 0.002 PHE D 391 TRP 0.021 0.002 TRP H 103 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (20466) covalent geometry : angle 0.77240 / 0.38 (27816) SS BOND : bond 0.00559 / 0.38 ( 39) SS BOND : angle 1.09625 / 0.79 ( 78) hydrogen bonds : bond 0.03594 / 2.44 ( 564) hydrogen bonds : angle 6.43264 / 4.44 ( 1539) link_ALPHA1-2 : bond 0.00516 / 0.29 ( 9) link_ALPHA1-2 : angle 2.08272 / 1.28 ( 27) link_ALPHA1-3 : bond 0.00081 / 0.04 ( 6) link_ALPHA1-3 : angle 1.44024 / 0.80 ( 18) link_ALPHA1-6 : bond 0.00081 / 0.04 ( 3) link_ALPHA1-6 : angle 1.51569 / 1.01 ( 9) link_BETA1-4 : bond 0.00448 / 0.24 ( 30) link_BETA1-4 : angle 1.98646 / 1.44 ( 90) link_NAG-ASN : bond 0.00705 / 0.43 ( 42) link_NAG-ASN : angle 2.32449 / 1.60 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9555 (OUTLIER) cc_final: 0.9164 (m100) REVERT: A 166 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7888 (tmm-80) REVERT: B 589 ASP cc_start: 0.9206 (p0) cc_final: 0.8881 (p0) REVERT: B 626 MET cc_start: 0.7568 (ptp) cc_final: 0.6965 (ptp) REVERT: B 647 GLU cc_start: 0.9342 (pt0) cc_final: 0.9098 (pp20) REVERT: B 648 GLU cc_start: 0.9598 (tt0) cc_final: 0.9081 (pt0) REVERT: H 100 GLU cc_start: 0.7909 (tt0) cc_final: 0.7669 (tt0) REVERT: C 69 TRP cc_start: 0.9563 (OUTLIER) cc_final: 0.8831 (m100) REVERT: E 589 ASP cc_start: 0.9243 (p0) cc_final: 0.8926 (p0) REVERT: E 648 GLU cc_start: 0.9502 (tt0) cc_final: 0.9066 (tp30) REVERT: E 654 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8484 (tm-30) REVERT: G 46 GLU cc_start: 0.8937 (tp30) cc_final: 0.8710 (tp30) REVERT: G 100 GLU cc_start: 0.8053 (tt0) cc_final: 0.7691 (tt0) REVERT: G 100 TYR cc_start: 0.8536 (m-10) cc_final: 0.8095 (m-10) REVERT: D 69 TRP cc_start: 0.9549 (OUTLIER) cc_final: 0.9276 (m100) REVERT: D 110 GLU cc_start: 0.9207 (tp30) cc_final: 0.8957 (tp30) REVERT: D 475 MET cc_start: 0.9105 (mmp) cc_final: 0.8840 (mmm) REVERT: F 589 ASP cc_start: 0.9161 (p0) cc_final: 0.8838 (p0) REVERT: F 626 MET cc_start: 0.7488 (ptp) cc_final: 0.7154 (ptp) REVERT: F 648 GLU cc_start: 0.9481 (tt0) cc_final: 0.9114 (pt0) REVERT: F 654 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8495 (tm-30) REVERT: I 20 LEU cc_start: 0.9021 (mp) cc_final: 0.8298 (tt) REVERT: I 100 TYR cc_start: 0.8564 (m-10) cc_final: 0.8269 (m-10) REVERT: I 100 MET cc_start: 0.7617 (ppp) cc_final: 0.7367 (ppp) outliers start: 44 outliers final: 25 residues processed: 179 average time/residue: 0.1477 time to fit residues: 41.5061 Evaluate side-chains 167 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 1 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.039499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.030458 restraints weight = 148931.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031518 restraints weight = 79473.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.032243 restraints weight = 52819.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032736 restraints weight = 40136.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033075 restraints weight = 33379.716| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20595 Z= 0.182 Angle : 0.722 14.094 28164 Z= 0.348 Chirality : 0.044 0.190 3393 Planarity : 0.004 0.041 3393 Dihedral : 5.451 26.249 2565 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.80 % Allowed : 10.92 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.17), residues: 2358 helix: -0.32 (0.27), residues: 426 sheet: -0.61 (0.20), residues: 681 loop : -2.20 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.013 0.001 TYR L 34 PHE 0.013 0.001 PHE D 391 TRP 0.016 0.002 TRP I 35 HIS 0.004 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (20466) covalent geometry : angle 0.70076 / 0.34 (27816) SS BOND : bond 0.00387 / 0.26 ( 39) SS BOND : angle 0.89647 / 0.64 ( 78) hydrogen bonds : bond 0.03297 / 2.23 ( 564) hydrogen bonds : angle 6.20092 / 4.27 ( 1539) link_ALPHA1-2 : bond 0.00175 / 0.10 ( 9) link_ALPHA1-2 : angle 1.76180 / 1.09 ( 27) link_ALPHA1-3 : bond 0.00185 / 0.09 ( 6) link_ALPHA1-3 : angle 1.45027 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00096 / 0.05 ( 3) link_ALPHA1-6 : angle 1.58404 / 1.08 ( 9) link_BETA1-4 : bond 0.00233 / 0.12 ( 30) link_BETA1-4 : angle 1.77567 / 1.28 ( 90) link_NAG-ASN : bond 0.00426 / 0.26 ( 42) link_NAG-ASN : angle 2.07253 / 1.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9550 (OUTLIER) cc_final: 0.9191 (m100) REVERT: A 166 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7817 (tmm-80) REVERT: B 589 ASP cc_start: 0.9215 (p0) cc_final: 0.8898 (p0) REVERT: B 626 MET cc_start: 0.7523 (ptp) cc_final: 0.6888 (ptp) REVERT: B 648 GLU cc_start: 0.9611 (tt0) cc_final: 0.9095 (pt0) REVERT: C 69 TRP cc_start: 0.9575 (OUTLIER) cc_final: 0.8889 (m100) REVERT: E 589 ASP cc_start: 0.9242 (p0) cc_final: 0.8930 (p0) REVERT: E 648 GLU cc_start: 0.9510 (tt0) cc_final: 0.9027 (tp30) REVERT: E 654 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8506 (tm-30) REVERT: G 46 GLU cc_start: 0.8958 (tp30) cc_final: 0.8733 (tp30) REVERT: G 100 GLU cc_start: 0.8064 (tt0) cc_final: 0.7591 (tt0) REVERT: G 100 TYR cc_start: 0.8453 (m-10) cc_final: 0.8128 (m-10) REVERT: D 65 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8065 (mmmt) REVERT: D 69 TRP cc_start: 0.9569 (OUTLIER) cc_final: 0.9336 (m100) REVERT: D 110 GLU cc_start: 0.9274 (tp30) cc_final: 0.8843 (tp30) REVERT: D 141 MET cc_start: 0.8981 (mmm) cc_final: 0.8724 (mmt) REVERT: D 475 MET cc_start: 0.9086 (mmp) cc_final: 0.8773 (mmm) REVERT: F 589 ASP cc_start: 0.9150 (p0) cc_final: 0.8825 (p0) REVERT: F 626 MET cc_start: 0.7511 (ptp) cc_final: 0.7178 (ptp) REVERT: F 648 GLU cc_start: 0.9492 (tt0) cc_final: 0.9054 (tp30) REVERT: F 654 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8456 (tm-30) REVERT: I 20 LEU cc_start: 0.9042 (mp) cc_final: 0.8338 (tt) REVERT: I 100 TYR cc_start: 0.8521 (m-10) cc_final: 0.8280 (m-80) REVERT: I 100 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7692 (t80) REVERT: I 100 MET cc_start: 0.7515 (ppp) cc_final: 0.7253 (ppp) outliers start: 38 outliers final: 20 residues processed: 179 average time/residue: 0.1455 time to fit residues: 40.6802 Evaluate side-chains 163 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 103 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 177 optimal weight: 0.0170 chunk 185 optimal weight: 10.0000 chunk 172 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 overall best weight: 2.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.030744 restraints weight = 148439.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031794 restraints weight = 78868.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032524 restraints weight = 52740.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033021 restraints weight = 39995.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033365 restraints weight = 33147.535| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20595 Z= 0.152 Angle : 0.709 13.408 28164 Z= 0.341 Chirality : 0.044 0.188 3393 Planarity : 0.004 0.037 3393 Dihedral : 5.282 25.349 2565 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.57 % Allowed : 11.73 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2358 helix: -0.28 (0.27), residues: 426 sheet: -0.48 (0.20), residues: 681 loop : -2.14 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 500 TYR 0.013 0.001 TYR L 34 PHE 0.012 0.001 PHE D 391 TRP 0.015 0.001 TRP H 35 HIS 0.003 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (20466) covalent geometry : angle 0.68831 / 0.34 (27816) SS BOND : bond 0.00334 / 0.22 ( 39) SS BOND : angle 1.07547 / 0.82 ( 78) hydrogen bonds : bond 0.03106 / 2.10 ( 564) hydrogen bonds : angle 6.01399 / 4.13 ( 1539) link_ALPHA1-2 : bond 0.00085 / 0.05 ( 9) link_ALPHA1-2 : angle 1.68834 / 1.05 ( 27) link_ALPHA1-3 : bond 0.00263 / 0.13 ( 6) link_ALPHA1-3 : angle 1.45887 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00148 / 0.07 ( 3) link_ALPHA1-6 : angle 1.54195 / 1.05 ( 9) link_BETA1-4 : bond 0.00275 / 0.15 ( 30) link_BETA1-4 : angle 1.68998 / 1.21 ( 90) link_NAG-ASN : bond 0.00321 / 0.19 ( 42) link_NAG-ASN : angle 1.94276 / 1.31 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9530 (OUTLIER) cc_final: 0.9150 (m100) REVERT: A 150 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8759 (mmt) REVERT: A 166 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7878 (tmm-80) REVERT: A 328 MET cc_start: 0.8682 (tpt) cc_final: 0.8411 (tpt) REVERT: B 589 ASP cc_start: 0.9184 (p0) cc_final: 0.8866 (p0) REVERT: B 626 MET cc_start: 0.7545 (ptp) cc_final: 0.7177 (ptp) REVERT: B 648 GLU cc_start: 0.9525 (tt0) cc_final: 0.9098 (pt0) REVERT: H 20 LEU cc_start: 0.9190 (mp) cc_final: 0.8554 (tt) REVERT: H 100 GLU cc_start: 0.7852 (tt0) cc_final: 0.7612 (tt0) REVERT: C 69 TRP cc_start: 0.9540 (OUTLIER) cc_final: 0.8845 (m100) REVERT: E 589 ASP cc_start: 0.9207 (p0) cc_final: 0.8877 (p0) REVERT: E 648 GLU cc_start: 0.9475 (tt0) cc_final: 0.8970 (tp30) REVERT: E 654 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8515 (tm-30) REVERT: G 46 GLU cc_start: 0.8894 (tp30) cc_final: 0.8681 (tp30) REVERT: G 100 GLU cc_start: 0.8046 (tt0) cc_final: 0.7607 (tt0) REVERT: G 100 TYR cc_start: 0.8418 (m-10) cc_final: 0.8121 (m-10) REVERT: G 100 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7675 (t80) REVERT: D 65 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8053 (mmmt) REVERT: D 110 GLU cc_start: 0.9230 (tp30) cc_final: 0.8787 (tp30) REVERT: F 589 ASP cc_start: 0.9116 (p0) cc_final: 0.8784 (p0) REVERT: F 626 MET cc_start: 0.7552 (ptp) cc_final: 0.7254 (ptp) REVERT: F 648 GLU cc_start: 0.9470 (tt0) cc_final: 0.9035 (tp30) REVERT: F 654 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8444 (tm-30) REVERT: I 20 LEU cc_start: 0.9051 (mp) cc_final: 0.8361 (tt) REVERT: I 100 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7707 (t80) REVERT: I 100 MET cc_start: 0.7477 (ppp) cc_final: 0.7213 (ppp) outliers start: 33 outliers final: 21 residues processed: 171 average time/residue: 0.1523 time to fit residues: 40.5445 Evaluate side-chains 171 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 212 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029920 restraints weight = 151145.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030957 restraints weight = 81162.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.031674 restraints weight = 54190.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.032161 restraints weight = 41226.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032493 restraints weight = 34355.334| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 20595 Z= 0.260 Angle : 0.778 12.446 28164 Z= 0.373 Chirality : 0.045 0.196 3393 Planarity : 0.004 0.036 3393 Dihedral : 5.410 26.021 2565 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 1.85 % Allowed : 11.63 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.17), residues: 2358 helix: -0.45 (0.26), residues: 435 sheet: -0.44 (0.20), residues: 681 loop : -2.18 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.014 0.001 TYR K 34 PHE 0.013 0.002 PHE A 391 TRP 0.018 0.002 TRP G 36 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 (20466) covalent geometry : angle 0.75547 / 0.37 (27816) SS BOND : bond 0.00486 / 0.35 ( 39) SS BOND : angle 0.94211 / 0.64 ( 78) hydrogen bonds : bond 0.03404 / 2.29 ( 564) hydrogen bonds : angle 6.04147 / 4.16 ( 1539) link_ALPHA1-2 : bond 0.00400 / 0.23 ( 9) link_ALPHA1-2 : angle 1.97434 / 1.22 ( 27) link_ALPHA1-3 : bond 0.00077 / 0.04 ( 6) link_ALPHA1-3 : angle 1.47544 / 0.83 ( 18) link_ALPHA1-6 : bond 0.00118 / 0.06 ( 3) link_ALPHA1-6 : angle 1.48366 / 0.99 ( 9) link_BETA1-4 : bond 0.00414 / 0.22 ( 30) link_BETA1-4 : angle 1.88101 / 1.37 ( 90) link_NAG-ASN : bond 0.00644 / 0.39 ( 42) link_NAG-ASN : angle 2.19919 / 1.50 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9525 (OUTLIER) cc_final: 0.9147 (m100) REVERT: A 150 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8355 (mmt) REVERT: A 166 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7951 (tmm-80) REVERT: B 589 ASP cc_start: 0.9201 (p0) cc_final: 0.8908 (p0) REVERT: B 626 MET cc_start: 0.7559 (ptp) cc_final: 0.7145 (ptp) REVERT: B 648 GLU cc_start: 0.9547 (tt0) cc_final: 0.9155 (pt0) REVERT: H 107 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8826 (p) REVERT: C 69 TRP cc_start: 0.9538 (OUTLIER) cc_final: 0.8877 (m100) REVERT: E 589 ASP cc_start: 0.9222 (p0) cc_final: 0.8923 (p0) REVERT: E 648 GLU cc_start: 0.9526 (tt0) cc_final: 0.9018 (tp30) REVERT: E 654 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8474 (tm-30) REVERT: G 46 GLU cc_start: 0.8946 (tp30) cc_final: 0.8734 (tp30) REVERT: G 100 GLU cc_start: 0.8079 (tt0) cc_final: 0.7668 (tt0) REVERT: G 100 TYR cc_start: 0.8523 (m-10) cc_final: 0.8163 (m-10) REVERT: G 100 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.7697 (t80) REVERT: D 110 GLU cc_start: 0.9242 (tp30) cc_final: 0.8917 (tp30) REVERT: D 195 ASN cc_start: 0.7689 (t0) cc_final: 0.7310 (t0) REVERT: D 475 MET cc_start: 0.8987 (mmp) cc_final: 0.8782 (mmm) REVERT: F 589 ASP cc_start: 0.9165 (p0) cc_final: 0.8860 (p0) REVERT: F 626 MET cc_start: 0.7515 (ptp) cc_final: 0.7225 (ptp) REVERT: F 648 GLU cc_start: 0.9467 (tt0) cc_final: 0.9000 (tp30) REVERT: F 654 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8725 (tm-30) REVERT: I 20 LEU cc_start: 0.8975 (mp) cc_final: 0.8339 (tt) REVERT: I 100 MET cc_start: 0.7480 (ppp) cc_final: 0.7171 (ppp) outliers start: 39 outliers final: 25 residues processed: 164 average time/residue: 0.1507 time to fit residues: 38.7893 Evaluate side-chains 158 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 81 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 135 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030240 restraints weight = 149749.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.031288 restraints weight = 79921.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032006 restraints weight = 53074.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.032500 restraints weight = 40302.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032819 restraints weight = 33501.605| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20595 Z= 0.200 Angle : 0.749 14.945 28164 Z= 0.358 Chirality : 0.045 0.187 3393 Planarity : 0.004 0.038 3393 Dihedral : 5.354 26.251 2565 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.57 % Allowed : 12.16 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2358 helix: -0.42 (0.26), residues: 435 sheet: -0.35 (0.20), residues: 681 loop : -2.16 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.014 0.001 TYR K 34 PHE 0.013 0.001 PHE A 391 TRP 0.016 0.002 TRP H 35 HIS 0.004 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (20466) covalent geometry : angle 0.72849 / 0.35 (27816) SS BOND : bond 0.00348 / 0.23 ( 39) SS BOND : angle 1.09376 / 0.82 ( 78) hydrogen bonds : bond 0.03213 / 2.18 ( 564) hydrogen bonds : angle 5.93984 / 4.09 ( 1539) link_ALPHA1-2 : bond 0.00201 / 0.12 ( 9) link_ALPHA1-2 : angle 1.79937 / 1.12 ( 27) link_ALPHA1-3 : bond 0.00161 / 0.07 ( 6) link_ALPHA1-3 : angle 1.47476 / 0.83 ( 18) link_ALPHA1-6 : bond 0.00116 / 0.06 ( 3) link_ALPHA1-6 : angle 1.53769 / 1.04 ( 9) link_BETA1-4 : bond 0.00279 / 0.15 ( 30) link_BETA1-4 : angle 1.74927 / 1.27 ( 90) link_NAG-ASN : bond 0.00477 / 0.28 ( 42) link_NAG-ASN : angle 2.06091 / 1.40 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9520 (OUTLIER) cc_final: 0.9192 (m100) REVERT: A 150 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8482 (mmp) REVERT: A 166 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7911 (tmm-80) REVERT: B 589 ASP cc_start: 0.9187 (p0) cc_final: 0.8898 (p0) REVERT: B 626 MET cc_start: 0.7577 (ptp) cc_final: 0.7157 (ptp) REVERT: B 648 GLU cc_start: 0.9550 (tt0) cc_final: 0.9162 (pt0) REVERT: H 100 GLU cc_start: 0.7835 (tt0) cc_final: 0.7570 (tt0) REVERT: C 69 TRP cc_start: 0.9533 (OUTLIER) cc_final: 0.8868 (m100) REVERT: E 589 ASP cc_start: 0.9224 (p0) cc_final: 0.8937 (p0) REVERT: E 648 GLU cc_start: 0.9493 (tt0) cc_final: 0.9010 (tp30) REVERT: E 654 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8501 (tm-30) REVERT: G 46 GLU cc_start: 0.8946 (tp30) cc_final: 0.8730 (tp30) REVERT: G 100 GLU cc_start: 0.8061 (tt0) cc_final: 0.7647 (tt0) REVERT: G 100 TYR cc_start: 0.8452 (m-10) cc_final: 0.8059 (m-10) REVERT: G 100 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7725 (t80) REVERT: D 65 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8003 (mmmt) REVERT: D 110 GLU cc_start: 0.9239 (tp30) cc_final: 0.8786 (tp30) REVERT: D 475 MET cc_start: 0.8988 (mmp) cc_final: 0.8731 (mmm) REVERT: F 589 ASP cc_start: 0.9134 (p0) cc_final: 0.8825 (p0) REVERT: F 626 MET cc_start: 0.7530 (ptp) cc_final: 0.7223 (ptp) REVERT: F 648 GLU cc_start: 0.9454 (tt0) cc_final: 0.9019 (tp30) REVERT: F 654 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8729 (tm-30) REVERT: I 20 LEU cc_start: 0.8999 (mp) cc_final: 0.8390 (tt) REVERT: I 100 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7643 (t80) REVERT: I 100 MET cc_start: 0.7424 (ppp) cc_final: 0.7111 (ppp) outliers start: 33 outliers final: 23 residues processed: 161 average time/residue: 0.1490 time to fit residues: 37.3972 Evaluate side-chains 163 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 150 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 213 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.030050 restraints weight = 150966.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031087 restraints weight = 80775.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031801 restraints weight = 53852.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032289 restraints weight = 40979.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032609 restraints weight = 34131.848| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20595 Z= 0.225 Angle : 0.763 14.412 28164 Z= 0.365 Chirality : 0.044 0.190 3393 Planarity : 0.004 0.036 3393 Dihedral : 5.334 26.014 2565 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.85 % Allowed : 11.97 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.17), residues: 2358 helix: -0.26 (0.27), residues: 417 sheet: -0.26 (0.20), residues: 681 loop : -2.19 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 327 TYR 0.014 0.001 TYR H 91 PHE 0.013 0.001 PHE A 391 TRP 0.017 0.002 TRP H 35 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (20466) covalent geometry : angle 0.74254 / 0.36 (27816) SS BOND : bond 0.00357 / 0.23 ( 39) SS BOND : angle 0.95390 / 0.69 ( 78) hydrogen bonds : bond 0.03240 / 2.19 ( 564) hydrogen bonds : angle 5.88962 / 4.05 ( 1539) link_ALPHA1-2 : bond 0.00269 / 0.16 ( 9) link_ALPHA1-2 : angle 1.85657 / 1.15 ( 27) link_ALPHA1-3 : bond 0.00135 / 0.06 ( 6) link_ALPHA1-3 : angle 1.47299 / 0.83 ( 18) link_ALPHA1-6 : bond 0.00107 / 0.05 ( 3) link_ALPHA1-6 : angle 1.51988 / 1.02 ( 9) link_BETA1-4 : bond 0.00331 / 0.18 ( 30) link_BETA1-4 : angle 1.78086 / 1.29 ( 90) link_NAG-ASN : bond 0.00544 / 0.32 ( 42) link_NAG-ASN : angle 2.12568 / 1.44 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.45 seconds wall clock time: 52 minutes 51.87 seconds (3171.87 seconds total)