Starting phenix.real_space_refine on Thu Jul 2 16:02:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.cif" model { file = "/net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8an3_15531/07_2026/8an3_15531.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 27 5.16 5 C 5529 2.51 5 N 1239 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8721 Number of models: 1 Model: "" Number of chains: 20 Chain: "AAA" Number of atoms: 7826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7826 Classifications: {'peptide': 1040} Link IDs: {'PCIS': 7, 'PTRANS': 64, 'TRANS': 968} Chain: "BBB" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "AAA" 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: 1.35, per 1000 atoms: 0.15 Number of scatterers: 8721 At special positions: 0 Unit cell: (138.6, 120.75, 127.05, 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 27 16.00 O 1926 8.00 N 1239 7.00 C 5529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSAAA 677 " - pdb=" SG CYSAAA1017 " distance=2.05 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 ?1-3 " NAG B 2 " - " YZT B 3 " " NAG E 2 " - " YZT E 3 " " NAG F 2 " - " YZT F 3 " " NAG G 2 " - " YZT G 3 " " NAG H 2 " - " YZT H 3 " " NAG I 2 " - " YZT I 3 " " NAG L 2 " - " YZT L 3 " " NAG M 2 " - " YZT M 3 " " NAG N 2 " - " YZT N 3 " " NAG P 2 " - " YZT P 3 " " NAG Q 2 " - " YZT Q 3 " " NAGBBB 2 " - " YZTBBB 3 " ALPHA1-4 " NAG B 2 " - " MAN B 5 " " NAG F 2 " - " MAN F 5 " " NAG H 2 " - " MAN H 4 " " NAG M 2 " - " MAN M 4 " " NAG P 2 " - " MAN P 4 " ALPHA1-6 " NAG B 2 " - " MAN B 6 " " NAG F 2 " - " MAN F 6 " " NAG G 2 " - " MAN G 4 " " NAG H 2 " - " MAN H 5 " " NAG I 2 " - " MAN I 4 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 5 " " NAG N 2 " - " MAN N 4 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 5 " " NAG Q 2 " - " MAN Q 4 " " NAGBBB 2 " - " MANBBB 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " YZT B 3 " - " BGC B 4 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " YZT F 3 " - " BGC F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAGBBB 1 " - " NAGBBB 2 " NAG-ASN " NAG A 1 " - " ASNAAA 70 " " NAG B 1 " - " ASNAAA 276 " " NAG C 1 " - " ASNAAA 295 " " NAG D 1 " - " ASNAAA 342 " " NAG E 1 " - " ASNAAA 358 " " NAG F 1 " - " ASNAAA 377 " " NAG G 1 " - " ASNAAA 468 " " NAG H 1 " - " ASNAAA 517 " " NAG I 1 " - " ASNAAA 545 " " NAG J 1 " - " ASNAAA 559 " " NAG K 1 " - " ASNAAA 581 " " NAG L 1 " - " ASNAAA 633 " " NAG M 1 " - " ASNAAA 714 " " NAG N 1 " - " ASNAAA 875 " " NAG O 1 " - " ASNAAA 914 " " NAG P 1 " - " ASNAAA 989 " " NAG Q 1 " - " ASNAAA1018 " " NAGAAA1501 " - " ASNAAA 955 " " NAGBBB 1 " - " ASNAAA 60 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 351.4 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 17 sheets defined 12.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'AAA' and resid 70 through 81 removed outlier: 4.003A pdb=" N ASNAAA 81 " --> pdb=" O THRAAA 77 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 139 through 143 removed outlier: 3.544A pdb=" N SERAAA 143 " --> pdb=" O LEUAAA 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'AAA' and resid 139 through 143' Processing helix chain 'AAA' and resid 144 through 145 No H-bonds generated for 'chain 'AAA' and resid 144 through 145' Processing helix chain 'AAA' and resid 146 through 151 Processing helix chain 'AAA' and resid 156 through 160 removed outlier: 3.776A pdb=" N GLYAAA 159 " --> pdb=" O ASPAAA 156 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALAAAA 160 " --> pdb=" O GLUAAA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'AAA' and resid 156 through 160' Processing helix chain 'AAA' and resid 171 through 173 No H-bonds generated for 'chain 'AAA' and resid 171 through 173' Processing helix chain 'AAA' and resid 186 through 193 Processing helix chain 'AAA' and resid 194 through 203 removed outlier: 4.411A pdb=" N ASNAAA 200 " --> pdb=" O THRAAA 196 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 248 through 253 Processing helix chain 'AAA' and resid 256 through 262 removed outlier: 3.644A pdb=" N LEUAAA 259 " --> pdb=" O LEUAAA 256 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLUAAA 262 " --> pdb=" O LEUAAA 259 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 617 through 619 No H-bonds generated for 'chain 'AAA' and resid 617 through 619' Processing helix chain 'AAA' and resid 620 through 628 removed outlier: 3.844A pdb=" N LEUAAA 625 " --> pdb=" O SERAAA 621 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 671 through 676 removed outlier: 3.559A pdb=" N ILEAAA 676 " --> pdb=" O GLNAAA 673 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 689 through 692 Processing helix chain 'AAA' and resid 764 through 769 removed outlier: 4.774A pdb=" N SERAAA 769 " --> pdb=" O ASNAAA 766 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 778 through 782 removed outlier: 3.502A pdb=" N PHEAAA 782 " --> pdb=" O ASNAAA 779 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 874 through 878 removed outlier: 3.571A pdb=" N PHEAAA 878 " --> pdb=" O ASNAAA 875 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 891 through 898 Processing helix chain 'AAA' and resid 940 through 943 Processing helix chain 'AAA' and resid 998 through 1006 removed outlier: 3.956A pdb=" N GLNAAA1003 " --> pdb=" O THRAAA 999 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THRAAA1004 " --> pdb=" O SERAAA1000 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 1026 through 1035 removed outlier: 4.142A pdb=" N LYSAAA1032 " --> pdb=" O THRAAA1028 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AAA' and resid 39 through 43 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 54 through 60 current: chain 'AAA' and resid 119 through 125 removed outlier: 8.943A pdb=" N THRAAA 168 " --> pdb=" O PHEAAA 121 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VALAAA 123 " --> pdb=" O THRAAA 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AAA' and resid 82 through 90 removed outlier: 3.858A pdb=" N GLYAAA 98 " --> pdb=" O THRAAA 88 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASNAAA 90 " --> pdb=" O THRAAA 96 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THRAAA 96 " --> pdb=" O ASNAAA 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 174 through 175 current: chain 'AAA' and resid 220 through 225 Processing sheet with id=AA3, first strand: chain 'AAA' and resid 136 through 138 removed outlier: 3.527A pdb=" N VALAAA 165 " --> pdb=" O ILEAAA 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AAA' and resid 236 through 237 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 236 through 237 current: chain 'AAA' and resid 274 through 280 Processing sheet with id=AA5, first strand: chain 'AAA' and resid 268 through 269 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 268 through 269 current: chain 'AAA' and resid 460 through 469 removed outlier: 6.091A pdb=" N ALAAAA 510 " --> pdb=" O GLUAAA 523 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLUAAA 523 " --> pdb=" O ALAAAA 510 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VALAAA 512 " --> pdb=" O THRAAA 521 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THRAAA 521 " --> pdb=" O VALAAA 512 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEUAAA 514 " --> pdb=" O THRAAA 519 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THRAAA 519 " --> pdb=" O LEUAAA 514 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 518 through 526 current: chain 'AAA' and resid 648 through 649 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 648 through 649 current: chain 'AAA' and resid 713 through 722 Processing sheet with id=AA6, first strand: chain 'AAA' and resid 302 through 314 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 336 through 341 current: chain 'AAA' and resid 364 through 374 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 364 through 374 current: chain 'AAA' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 414 through 420 current: chain 'AAA' and resid 548 through 560 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 564 through 570 current: chain 'AAA' and resid 581 through 584 Processing sheet with id=AA7, first strand: chain 'AAA' and resid 321 through 324 removed outlier: 6.731A pdb=" N PHEAAA 322 " --> pdb=" O THRAAA 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AAA' and resid 346 through 348 removed outlier: 3.884A pdb=" N LEUAAA 351 " --> pdb=" O ALAAAA 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AAA' and resid 389 through 393 Processing sheet with id=AB1, first strand: chain 'AAA' and resid 664 through 667 Processing sheet with id=AB2, first strand: chain 'AAA' and resid 725 through 726 removed outlier: 3.971A pdb=" N THRAAA 745 " --> pdb=" O VALAAA 726 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'AAA' and resid 748 through 751 Processing sheet with id=AB4, first strand: chain 'AAA' and resid 785 through 786 Processing sheet with id=AB5, first strand: chain 'AAA' and resid 805 through 807 removed outlier: 3.857A pdb=" N ALAAAA 805 " --> pdb=" O ALAAAA 800 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AAA' and resid 852 through 853 Processing sheet with id=AB7, first strand: chain 'AAA' and resid 918 through 920 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 918 through 920 current: chain 'AAA' and resid 957 through 961 removed outlier: 6.909A pdb=" N SERAAA 958 " --> pdb=" O LEUAAA 977 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 992 through 994 current: chain 'AAA' and resid 1018 through 1023 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 1018 through 1023 current: chain 'AAA' and resid 1058 through 1066 Processing sheet with id=AB8, first strand: chain 'AAA' and resid 966 through 967 156 hydrogen bonds defined for protein. 378 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: 1.67 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1498 1.33 - 1.46: 3039 1.46 - 1.58: 4345 1.58 - 1.71: 1 1.71 - 1.84: 40 Bond restraints: 8923 Sorted by residual: bond pdb=" C ASNAAA 248 " pdb=" O ASNAAA 248 " ideal model delta sigma weight residual 1.246 1.208 0.038 9.20e-03 1.18e+04 1.68e+01 bond pdb=" S6 YZTBBB 3 " pdb="O3S6 YZTBBB 3 " ideal model delta sigma weight residual 1.473 1.551 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" S6 YZT Q 3 " pdb="O1S6 YZT Q 3 " ideal model delta sigma weight residual 1.477 1.553 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" S6 YZT P 3 " pdb="O1S6 YZT P 3 " ideal model delta sigma weight residual 1.477 1.553 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" S6 YZT L 3 " pdb="O3S6 YZT L 3 " ideal model delta sigma weight residual 1.473 1.548 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 8918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 11747 3.99 - 7.99: 519 7.99 - 11.98: 25 11.98 - 15.98: 3 15.98 - 19.97: 2 Bond angle restraints: 12296 Sorted by residual: angle pdb=" C GLNAAA 825 " pdb=" N VALAAA 826 " pdb=" CA VALAAA 826 " ideal model delta sigma weight residual 120.24 126.97 -6.73 6.30e-01 2.52e+00 1.14e+02 angle pdb=" CA ASNAAA 545 " pdb=" CB ASNAAA 545 " pdb=" CG ASNAAA 545 " ideal model delta sigma weight residual 112.60 120.07 -7.47 1.00e+00 1.00e+00 5.57e+01 angle pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sigma weight residual 113.21 133.18 -19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" C PROAAA 695 " pdb=" CA PROAAA 695 " pdb=" CB PROAAA 695 " ideal model delta sigma weight residual 111.85 102.58 9.27 1.42e+00 4.96e-01 4.26e+01 angle pdb=" CA ASNAAA 914 " pdb=" CB ASNAAA 914 " pdb=" CG ASNAAA 914 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.00e+00 1.00e+00 4.17e+01 ... (remaining 12291 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.36: 4368 17.36 - 34.72: 274 34.72 - 52.07: 48 52.07 - 69.43: 11 69.43 - 86.78: 8 Dihedral angle restraints: 4709 sinusoidal: 1677 harmonic: 3032 Sorted by residual: dihedral pdb=" C THRAAA 548 " pdb=" N THRAAA 548 " pdb=" CA THRAAA 548 " pdb=" CB THRAAA 548 " ideal model delta harmonic sigma weight residual -122.00 -106.02 -15.98 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C THRAAA 516 " pdb=" N THRAAA 516 " pdb=" CA THRAAA 516 " pdb=" CB THRAAA 516 " ideal model delta harmonic sigma weight residual -122.00 -137.75 15.75 0 2.50e+00 1.60e-01 3.97e+01 dihedral pdb=" C THRAAA 386 " pdb=" N THRAAA 386 " pdb=" CA THRAAA 386 " pdb=" CB THRAAA 386 " ideal model delta harmonic sigma weight residual -122.00 -137.40 15.40 0 2.50e+00 1.60e-01 3.79e+01 ... (remaining 4706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 1609 0.285 - 0.571: 53 0.571 - 0.856: 3 0.856 - 1.142: 2 1.142 - 1.427: 2 Chirality restraints: 1669 Sorted by residual: chirality pdb=" C1 MAN P 5 " pdb=" O6 NAG P 2 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 1.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.20e+02 chirality pdb=" C1 MAN B 5 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 5 " pdb=" O5 MAN B 5 " both_signs ideal model delta sigma weight residual False 2.40 2.07 0.33 2.00e-02 2.50e+03 2.80e+02 ... (remaining 1666 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.332 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG H 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.322 2.00e-02 2.50e+03 2.82e-01 9.97e+02 pdb=" C7 NAG F 1 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAGBBB 2 " -0.320 2.00e-02 2.50e+03 2.70e-01 9.13e+02 pdb=" C7 NAGBBB 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAGBBB 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAGBBB 2 " 0.470 2.00e-02 2.50e+03 pdb=" O7 NAGBBB 2 " -0.046 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 2 2.15 - 2.84: 2336 2.84 - 3.52: 10871 3.52 - 4.21: 20668 4.21 - 4.90: 32740 Nonbonded interactions: 66617 Sorted by model distance: nonbonded pdb=" OD1 ASNAAA 581 " pdb=" C1 NAG K 1 " model vdw 1.460 2.776 nonbonded pdb=" OD1 ASNAAA 545 " pdb=" C1 NAG I 1 " model vdw 1.770 2.776 nonbonded pdb=" O5 NAG P 2 " pdb=" O6 NAG P 2 " model vdw 2.279 2.432 nonbonded pdb=" OD1 ASNAAA 581 " pdb=" C2 NAG K 1 " model vdw 2.352 3.470 nonbonded pdb=" O SERAAA 408 " pdb=" O6 NAG E 1 " model vdw 2.387 3.040 ... (remaining 66612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'BBB') selection = chain 'G' selection = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.012 0.092 8992 Z= 0.678 Angle : 2.050 50.101 12502 Z= 1.134 Chirality : 0.144 1.427 1669 Planarity : 0.030 0.283 1435 Dihedral : 12.949 86.781 2790 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.45 % Allowed : 3.91 % Favored : 95.65 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 9.86 % 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: -1.24 (0.24), residues: 1038 helix: -2.55 (0.42), residues: 74 sheet: 0.14 (0.24), residues: 410 loop : -1.33 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.007 ARGAAA 272 TYR 0.048 0.007 TYRAAA 541 PHE 0.036 0.007 PHEAAA 126 TRP 0.048 0.013 TRPAAA 311 HIS 0.018 0.009 HISAAA1051 Details of bonding type rmsd/Z covalent geometry : bond 0.01140 / 0.67 ( 8923) covalent geometry : angle 1.89807 / 1.11 (12296) SS BOND : bond 0.02157 / 1.14 ( 1) SS BOND : angle 1.45343 / 0.78 ( 2) hydrogen bonds : bond 0.22522 / 15.07 ( 156) hydrogen bonds : angle 7.35025 / 4.99 ( 378) glycosidic custom : bond 0.02604 / 1.90 ( 12) glycosidic custom : angle 4.68286 / 3.90 ( 36) link_ALPHA1-4 : bond 0.01739 / 0.99 ( 5) link_ALPHA1-4 : angle 2.61454 / 1.33 ( 15) link_ALPHA1-6 : bond 0.02075 / 1.41 ( 12) link_ALPHA1-6 : angle 3.22879 / 2.09 ( 36) link_BETA1-4 : bond 0.01302 / 0.89 ( 20) link_BETA1-4 : angle 3.51627 / 2.39 ( 60) link_NAG-ASN : bond 0.02965 / 2.84 ( 19) link_NAG-ASN : angle 10.43872 / 5.75 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 313 time to evaluate : 0.298 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: AAA 141 TYR cc_start: 0.8967 (t80) cc_final: 0.8750 (t80) REVERT: AAA 209 SER cc_start: 0.9000 (p) cc_final: 0.8797 (t) REVERT: AAA 232 TYR cc_start: 0.8632 (p90) cc_final: 0.7821 (p90) REVERT: AAA 239 ASN cc_start: 0.8677 (m110) cc_final: 0.8284 (t0) REVERT: AAA 243 GLN cc_start: 0.8829 (mt0) cc_final: 0.8523 (mm-40) REVERT: AAA 253 ASN cc_start: 0.8953 (m-40) cc_final: 0.8392 (p0) REVERT: AAA 258 SER cc_start: 0.8341 (t) cc_final: 0.8116 (m) REVERT: AAA 262 GLU cc_start: 0.8896 (pt0) cc_final: 0.8659 (pm20) REVERT: AAA 308 GLN cc_start: 0.8132 (tt0) cc_final: 0.7232 (tt0) REVERT: AAA 316 ASN cc_start: 0.9134 (p0) cc_final: 0.8717 (t0) REVERT: AAA 322 PHE cc_start: 0.8746 (p90) cc_final: 0.8341 (p90) REVERT: AAA 337 LEU cc_start: 0.8914 (tp) cc_final: 0.8537 (mm) REVERT: AAA 340 ILE cc_start: 0.8736 (mt) cc_final: 0.8519 (mm) REVERT: AAA 389 VAL cc_start: 0.8376 (t) cc_final: 0.7878 (m) REVERT: AAA 430 THR cc_start: 0.8598 (m) cc_final: 0.8335 (p) REVERT: AAA 487 SER cc_start: 0.8686 (p) cc_final: 0.8468 (t) REVERT: AAA 500 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8101 (pp30) REVERT: AAA 548 THR cc_start: 0.8577 (m) cc_final: 0.8235 (p) REVERT: AAA 571 SER cc_start: 0.8093 (p) cc_final: 0.7835 (m) REVERT: AAA 575 MET cc_start: 0.8250 (mtp) cc_final: 0.7922 (mtp) REVERT: AAA 579 ASN cc_start: 0.7865 (t0) cc_final: 0.7501 (t0) REVERT: AAA 580 ASN cc_start: 0.7502 (m110) cc_final: 0.7108 (t0) REVERT: AAA 613 GLU cc_start: 0.8724 (tt0) cc_final: 0.8513 (tt0) REVERT: AAA 636 SER cc_start: 0.8552 (p) cc_final: 0.8146 (m) REVERT: AAA 646 ASN cc_start: 0.8471 (m-40) cc_final: 0.8122 (m110) REVERT: AAA 660 VAL cc_start: 0.8568 (t) cc_final: 0.8324 (p) REVERT: AAA 706 LEU cc_start: 0.8259 (mt) cc_final: 0.7955 (mp) REVERT: AAA 714 ASN cc_start: 0.8497 (m-40) cc_final: 0.8120 (p0) REVERT: AAA 721 PHE cc_start: 0.8792 (m-80) cc_final: 0.8566 (m-80) REVERT: AAA 727 TYR cc_start: 0.8627 (m-80) cc_final: 0.8331 (m-10) REVERT: AAA 778 ASP cc_start: 0.9063 (p0) cc_final: 0.8774 (p0) REVERT: AAA 793 MET cc_start: 0.8451 (mmt) cc_final: 0.8188 (mmt) REVERT: AAA 797 SER cc_start: 0.8848 (t) cc_final: 0.8512 (p) REVERT: AAA 841 ASN cc_start: 0.8413 (m-40) cc_final: 0.8166 (m-40) REVERT: AAA 858 ILE cc_start: 0.8216 (mm) cc_final: 0.7878 (mt) REVERT: AAA 859 ASN cc_start: 0.8257 (t0) cc_final: 0.7996 (t0) REVERT: AAA 872 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8343 (p) REVERT: AAA 882 ASN cc_start: 0.8826 (p0) cc_final: 0.8489 (p0) REVERT: AAA 883 ILE cc_start: 0.8761 (mt) cc_final: 0.8466 (mm) REVERT: AAA 888 THR cc_start: 0.8821 (m) cc_final: 0.8447 (p) REVERT: AAA 936 TYR cc_start: 0.7660 (m-80) cc_final: 0.7442 (m-80) REVERT: AAA 939 GLU cc_start: 0.9044 (tt0) cc_final: 0.8834 (tm-30) outliers start: 4 outliers final: 1 residues processed: 316 average time/residue: 0.0691 time to fit residues: 33.1828 Evaluate side-chains 262 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.133553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103830 restraints weight = 17752.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107985 restraints weight = 9935.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110780 restraints weight = 6659.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112675 restraints weight = 5044.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113993 restraints weight = 4145.590| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8992 Z= 0.167 Angle : 0.958 13.341 12502 Z= 0.419 Chirality : 0.053 0.380 1669 Planarity : 0.005 0.062 1435 Dihedral : 6.086 25.115 1157 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.90 % Allowed : 12.28 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1038 helix: -1.83 (0.43), residues: 87 sheet: 0.63 (0.24), residues: 436 loop : -0.96 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 272 TYR 0.018 0.002 TYRAAA 696 PHE 0.017 0.002 PHEAAA 747 TRP 0.035 0.004 TRPAAA 433 HIS 0.006 0.002 HISAAA1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 8923) covalent geometry : angle 0.90316 / 0.41 (12296) SS BOND : bond 0.00686 / 0.36 ( 1) SS BOND : angle 4.05283 / 2.27 ( 2) hydrogen bonds : bond 0.04315 / 2.84 ( 156) hydrogen bonds : angle 5.86919 / 4.00 ( 378) glycosidic custom : bond 0.00239 / 0.16 ( 12) glycosidic custom : angle 2.13110 / 1.37 ( 36) link_ALPHA1-4 : bond 0.00643 / 0.37 ( 5) link_ALPHA1-4 : angle 1.63084 / 0.85 ( 15) link_ALPHA1-6 : bond 0.00672 / 0.40 ( 12) link_ALPHA1-6 : angle 2.26012 / 1.40 ( 36) link_BETA1-4 : bond 0.00762 / 0.54 ( 20) link_BETA1-4 : angle 2.17975 / 1.32 ( 60) link_NAG-ASN : bond 0.00774 / 0.42 ( 19) link_NAG-ASN : angle 3.60790 / 2.21 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 232 TYR cc_start: 0.7338 (p90) cc_final: 0.6498 (p90) REVERT: AAA 243 GLN cc_start: 0.7818 (mt0) cc_final: 0.7480 (mp10) REVERT: AAA 253 ASN cc_start: 0.7189 (m-40) cc_final: 0.6904 (t0) REVERT: AAA 314 SER cc_start: 0.7655 (m) cc_final: 0.7368 (t) REVERT: AAA 316 ASN cc_start: 0.8289 (p0) cc_final: 0.8004 (p0) REVERT: AAA 333 TYR cc_start: 0.7964 (t80) cc_final: 0.7714 (t80) REVERT: AAA 334 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7500 (mt-10) REVERT: AAA 337 LEU cc_start: 0.8247 (tp) cc_final: 0.7805 (mt) REVERT: AAA 389 VAL cc_start: 0.8075 (t) cc_final: 0.7626 (m) REVERT: AAA 425 THR cc_start: 0.8038 (m) cc_final: 0.7540 (p) REVERT: AAA 426 THR cc_start: 0.8282 (p) cc_final: 0.8021 (t) REVERT: AAA 430 THR cc_start: 0.7887 (m) cc_final: 0.7672 (p) REVERT: AAA 452 ASN cc_start: 0.7514 (m-40) cc_final: 0.7143 (m-40) REVERT: AAA 478 SER cc_start: 0.8377 (m) cc_final: 0.7990 (p) REVERT: AAA 487 SER cc_start: 0.8121 (p) cc_final: 0.7911 (t) REVERT: AAA 580 ASN cc_start: 0.7399 (m110) cc_final: 0.6900 (t0) REVERT: AAA 613 GLU cc_start: 0.7339 (tt0) cc_final: 0.7009 (tt0) REVERT: AAA 636 SER cc_start: 0.8296 (p) cc_final: 0.7857 (m) REVERT: AAA 642 TYR cc_start: 0.8036 (t80) cc_final: 0.7634 (t80) REVERT: AAA 643 ASP cc_start: 0.7145 (t0) cc_final: 0.6535 (t0) REVERT: AAA 646 ASN cc_start: 0.7759 (m-40) cc_final: 0.7289 (m110) REVERT: AAA 660 VAL cc_start: 0.7809 (t) cc_final: 0.7458 (p) REVERT: AAA 688 ASP cc_start: 0.7826 (t0) cc_final: 0.7481 (t0) REVERT: AAA 706 LEU cc_start: 0.7334 (mt) cc_final: 0.6910 (mp) REVERT: AAA 714 ASN cc_start: 0.7088 (m-40) cc_final: 0.6680 (p0) REVERT: AAA 726 VAL cc_start: 0.7801 (t) cc_final: 0.7450 (p) REVERT: AAA 727 TYR cc_start: 0.7889 (m-80) cc_final: 0.7419 (m-80) REVERT: AAA 768 LEU cc_start: 0.8662 (mt) cc_final: 0.8363 (mt) REVERT: AAA 797 SER cc_start: 0.8350 (t) cc_final: 0.7704 (p) REVERT: AAA 828 SER cc_start: 0.8472 (m) cc_final: 0.7702 (p) REVERT: AAA 841 ASN cc_start: 0.8052 (m-40) cc_final: 0.7683 (m-40) REVERT: AAA 859 ASN cc_start: 0.6974 (t0) cc_final: 0.6473 (t0) REVERT: AAA 872 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8141 (p) REVERT: AAA 882 ASN cc_start: 0.7456 (p0) cc_final: 0.6793 (t0) REVERT: AAA 883 ILE cc_start: 0.8361 (mt) cc_final: 0.7803 (mm) REVERT: AAA 884 LYS cc_start: 0.8278 (tttt) cc_final: 0.8013 (tttm) REVERT: AAA 907 PHE cc_start: 0.7060 (m-10) cc_final: 0.6813 (m-10) REVERT: AAA 909 THR cc_start: 0.7598 (t) cc_final: 0.6475 (t) REVERT: AAA 912 VAL cc_start: 0.8649 (t) cc_final: 0.8301 (p) REVERT: AAA 1030 LEU cc_start: 0.8061 (tp) cc_final: 0.7849 (pp) outliers start: 26 outliers final: 14 residues processed: 279 average time/residue: 0.0699 time to fit residues: 29.7061 Evaluate side-chains 267 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 96 THR Chi-restraints excluded: chain AAA residue 144 LYS Chi-restraints excluded: chain AAA residue 176 THR Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 679 ASN Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.125684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096495 restraints weight = 17737.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100376 restraints weight = 10062.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102951 restraints weight = 6830.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104753 restraints weight = 5225.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105772 restraints weight = 4334.903| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8992 Z= 0.274 Angle : 0.928 14.370 12502 Z= 0.429 Chirality : 0.053 0.251 1669 Planarity : 0.006 0.065 1435 Dihedral : 6.339 27.823 1157 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.02 % Allowed : 14.17 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1038 helix: -1.81 (0.48), residues: 83 sheet: 0.40 (0.25), residues: 422 loop : -1.23 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGAAA 272 TYR 0.031 0.002 TYRAAA 296 PHE 0.016 0.002 PHEAAA 322 TRP 0.018 0.004 TRPAAA 631 HIS 0.003 0.002 HISAAA 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 ( 8923) covalent geometry : angle 0.88515 / 0.42 (12296) SS BOND : bond 0.00368 / 0.19 ( 1) SS BOND : angle 3.33615 / 1.83 ( 2) hydrogen bonds : bond 0.05533 / 3.63 ( 156) hydrogen bonds : angle 6.19985 / 4.30 ( 378) glycosidic custom : bond 0.00335 / 0.19 ( 12) glycosidic custom : angle 1.82506 / 1.10 ( 36) link_ALPHA1-4 : bond 0.00532 / 0.29 ( 5) link_ALPHA1-4 : angle 1.71455 / 0.91 ( 15) link_ALPHA1-6 : bond 0.00567 / 0.33 ( 12) link_ALPHA1-6 : angle 1.94545 / 1.23 ( 36) link_BETA1-4 : bond 0.00673 / 0.42 ( 20) link_BETA1-4 : angle 2.20703 / 1.27 ( 60) link_NAG-ASN : bond 0.00653 / 0.34 ( 19) link_NAG-ASN : angle 2.99749 / 1.82 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 128 TYR cc_start: 0.7908 (t80) cc_final: 0.7536 (t80) REVERT: AAA 232 TYR cc_start: 0.7542 (p90) cc_final: 0.7097 (p90) REVERT: AAA 243 GLN cc_start: 0.7694 (mt0) cc_final: 0.7482 (mp10) REVERT: AAA 253 ASN cc_start: 0.7416 (m-40) cc_final: 0.7029 (m-40) REVERT: AAA 280 ILE cc_start: 0.8698 (mt) cc_final: 0.8365 (pt) REVERT: AAA 306 MET cc_start: 0.7129 (mtt) cc_final: 0.6780 (mtt) REVERT: AAA 314 SER cc_start: 0.7795 (m) cc_final: 0.7083 (p) REVERT: AAA 316 ASN cc_start: 0.8212 (p0) cc_final: 0.7692 (p0) REVERT: AAA 334 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7521 (mt-10) REVERT: AAA 369 TYR cc_start: 0.6764 (m-10) cc_final: 0.6553 (m-10) REVERT: AAA 389 VAL cc_start: 0.7951 (t) cc_final: 0.7470 (m) REVERT: AAA 426 THR cc_start: 0.8299 (p) cc_final: 0.8063 (t) REVERT: AAA 452 ASN cc_start: 0.7666 (m-40) cc_final: 0.7327 (m-40) REVERT: AAA 478 SER cc_start: 0.8346 (m) cc_final: 0.7964 (p) REVERT: AAA 498 THR cc_start: 0.7054 (t) cc_final: 0.6718 (p) REVERT: AAA 520 LEU cc_start: 0.7960 (mm) cc_final: 0.7650 (mm) REVERT: AAA 541 TYR cc_start: 0.6961 (m-10) cc_final: 0.6481 (m-10) REVERT: AAA 550 MET cc_start: 0.6782 (ttt) cc_final: 0.6453 (ttt) REVERT: AAA 575 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6558 (tpp) REVERT: AAA 627 ASP cc_start: 0.7687 (m-30) cc_final: 0.7487 (m-30) REVERT: AAA 630 LEU cc_start: 0.8526 (mt) cc_final: 0.8203 (mm) REVERT: AAA 636 SER cc_start: 0.8358 (p) cc_final: 0.8033 (m) REVERT: AAA 643 ASP cc_start: 0.7337 (t0) cc_final: 0.6661 (t70) REVERT: AAA 660 VAL cc_start: 0.7942 (t) cc_final: 0.7626 (p) REVERT: AAA 686 ILE cc_start: 0.8477 (mt) cc_final: 0.8134 (mp) REVERT: AAA 688 ASP cc_start: 0.8037 (t0) cc_final: 0.7715 (t70) REVERT: AAA 706 LEU cc_start: 0.7563 (mt) cc_final: 0.7175 (mp) REVERT: AAA 714 ASN cc_start: 0.6946 (m-40) cc_final: 0.6368 (p0) REVERT: AAA 726 VAL cc_start: 0.8159 (t) cc_final: 0.7805 (p) REVERT: AAA 727 TYR cc_start: 0.7927 (m-80) cc_final: 0.7421 (m-80) REVERT: AAA 797 SER cc_start: 0.8333 (t) cc_final: 0.7806 (p) REVERT: AAA 798 ILE cc_start: 0.8301 (mt) cc_final: 0.8039 (mp) REVERT: AAA 828 SER cc_start: 0.8782 (m) cc_final: 0.7770 (p) REVERT: AAA 838 TYR cc_start: 0.7715 (m-80) cc_final: 0.7257 (m-80) REVERT: AAA 859 ASN cc_start: 0.7514 (t0) cc_final: 0.7059 (t0) REVERT: AAA 872 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8295 (p) REVERT: AAA 883 ILE cc_start: 0.8597 (mt) cc_final: 0.8274 (mm) REVERT: AAA 884 LYS cc_start: 0.8438 (tttt) cc_final: 0.8236 (tttm) REVERT: AAA 920 TYR cc_start: 0.7822 (p90) cc_final: 0.7557 (p90) REVERT: AAA 939 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6799 (tm-30) REVERT: AAA 980 ILE cc_start: 0.9110 (mm) cc_final: 0.8819 (tp) outliers start: 36 outliers final: 25 residues processed: 286 average time/residue: 0.0696 time to fit residues: 30.4854 Evaluate side-chains 267 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 34 VAL Chi-restraints excluded: chain AAA residue 96 THR Chi-restraints excluded: chain AAA residue 123 VAL Chi-restraints excluded: chain AAA residue 176 THR Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 309 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 382 VAL Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 806 SER Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 950 ILE Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.127309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098041 restraints weight = 17899.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101957 restraints weight = 10064.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104618 restraints weight = 6817.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106423 restraints weight = 5201.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107447 restraints weight = 4298.659| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8992 Z= 0.159 Angle : 0.850 12.043 12502 Z= 0.384 Chirality : 0.048 0.222 1669 Planarity : 0.005 0.066 1435 Dihedral : 5.881 49.202 1157 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 3.79 % Allowed : 17.19 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1038 helix: -1.60 (0.51), residues: 83 sheet: 0.45 (0.25), residues: 437 loop : -1.17 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAAA 272 TYR 0.024 0.001 TYRAAA 392 PHE 0.021 0.002 PHEAAA 738 TRP 0.026 0.003 TRPAAA 433 HIS 0.003 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 8923) covalent geometry : angle 0.79821 / 0.37 (12296) SS BOND : bond 0.01147 / 0.60 ( 1) SS BOND : angle 5.05998 / 2.74 ( 2) hydrogen bonds : bond 0.04038 / 2.69 ( 156) hydrogen bonds : angle 6.20550 / 4.32 ( 378) glycosidic custom : bond 0.00247 / 0.19 ( 12) glycosidic custom : angle 1.83795 / 1.39 ( 36) link_ALPHA1-4 : bond 0.00582 / 0.33 ( 5) link_ALPHA1-4 : angle 1.53489 / 0.84 ( 15) link_ALPHA1-6 : bond 0.00562 / 0.34 ( 12) link_ALPHA1-6 : angle 1.86816 / 1.21 ( 36) link_BETA1-4 : bond 0.00618 / 0.41 ( 20) link_BETA1-4 : angle 2.32157 / 1.44 ( 60) link_NAG-ASN : bond 0.00676 / 0.38 ( 19) link_NAG-ASN : angle 3.05716 / 1.84 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.298 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: AAA 243 GLN cc_start: 0.7727 (mt0) cc_final: 0.7477 (mp10) REVERT: AAA 253 ASN cc_start: 0.7301 (m-40) cc_final: 0.6936 (m-40) REVERT: AAA 288 VAL cc_start: 0.8355 (t) cc_final: 0.8037 (p) REVERT: AAA 314 SER cc_start: 0.7829 (m) cc_final: 0.7422 (p) REVERT: AAA 316 ASN cc_start: 0.8264 (p0) cc_final: 0.7817 (p0) REVERT: AAA 334 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7328 (mt-10) REVERT: AAA 389 VAL cc_start: 0.7921 (t) cc_final: 0.7466 (m) REVERT: AAA 426 THR cc_start: 0.8253 (p) cc_final: 0.8024 (t) REVERT: AAA 444 VAL cc_start: 0.8706 (t) cc_final: 0.8395 (p) REVERT: AAA 452 ASN cc_start: 0.7684 (m-40) cc_final: 0.7350 (m-40) REVERT: AAA 478 SER cc_start: 0.8349 (m) cc_final: 0.7980 (p) REVERT: AAA 498 THR cc_start: 0.7158 (t) cc_final: 0.6814 (p) REVERT: AAA 520 LEU cc_start: 0.7921 (mm) cc_final: 0.7577 (mm) REVERT: AAA 541 TYR cc_start: 0.6844 (m-10) cc_final: 0.6415 (m-10) REVERT: AAA 550 MET cc_start: 0.6753 (ttt) cc_final: 0.6139 (ttt) REVERT: AAA 575 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6552 (tpp) REVERT: AAA 611 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6495 (mp10) REVERT: AAA 612 LEU cc_start: 0.7885 (tt) cc_final: 0.7587 (tp) REVERT: AAA 630 LEU cc_start: 0.8583 (mt) cc_final: 0.8274 (mm) REVERT: AAA 636 SER cc_start: 0.8249 (p) cc_final: 0.7973 (m) REVERT: AAA 643 ASP cc_start: 0.7135 (t0) cc_final: 0.6697 (t0) REVERT: AAA 660 VAL cc_start: 0.7910 (t) cc_final: 0.7596 (p) REVERT: AAA 706 LEU cc_start: 0.7479 (mt) cc_final: 0.7131 (mp) REVERT: AAA 714 ASN cc_start: 0.7003 (m-40) cc_final: 0.6543 (p0) REVERT: AAA 726 VAL cc_start: 0.8020 (t) cc_final: 0.7664 (p) REVERT: AAA 727 TYR cc_start: 0.7901 (m-80) cc_final: 0.7393 (m-10) REVERT: AAA 797 SER cc_start: 0.8309 (t) cc_final: 0.7724 (p) REVERT: AAA 798 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7963 (mp) REVERT: AAA 828 SER cc_start: 0.8678 (m) cc_final: 0.7663 (p) REVERT: AAA 859 ASN cc_start: 0.7402 (t0) cc_final: 0.6936 (t0) REVERT: AAA 872 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8271 (p) REVERT: AAA 884 LYS cc_start: 0.8309 (tttt) cc_final: 0.8090 (tttm) REVERT: AAA 920 TYR cc_start: 0.7851 (p90) cc_final: 0.7484 (p90) REVERT: AAA 939 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6882 (tm-30) REVERT: AAA 974 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7364 (mm-40) outliers start: 34 outliers final: 23 residues processed: 270 average time/residue: 0.0681 time to fit residues: 27.9170 Evaluate side-chains 263 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 34 VAL Chi-restraints excluded: chain AAA residue 96 THR Chi-restraints excluded: chain AAA residue 123 VAL Chi-restraints excluded: chain AAA residue 176 THR Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 361 ILE Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 611 GLN Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098071 restraints weight = 17637.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102028 restraints weight = 10001.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104700 restraints weight = 6788.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.106504 restraints weight = 5191.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107681 restraints weight = 4308.038| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8992 Z= 0.158 Angle : 0.816 12.875 12502 Z= 0.370 Chirality : 0.050 0.421 1669 Planarity : 0.005 0.067 1435 Dihedral : 5.619 40.422 1157 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.35 % Allowed : 20.65 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1038 helix: -1.45 (0.54), residues: 77 sheet: 0.32 (0.25), residues: 435 loop : -1.19 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 272 TYR 0.025 0.001 TYRAAA 128 PHE 0.026 0.002 PHEAAA 979 TRP 0.035 0.003 TRPAAA 433 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 8923) covalent geometry : angle 0.77866 / 0.36 (12296) SS BOND : bond 0.00938 / 0.49 ( 1) SS BOND : angle 4.77412 / 2.53 ( 2) hydrogen bonds : bond 0.03796 / 2.56 ( 156) hydrogen bonds : angle 5.99758 / 4.19 ( 378) glycosidic custom : bond 0.00331 / 0.25 ( 12) glycosidic custom : angle 1.43987 / 0.85 ( 36) link_ALPHA1-4 : bond 0.00615 / 0.36 ( 5) link_ALPHA1-4 : angle 1.56084 / 0.86 ( 15) link_ALPHA1-6 : bond 0.00629 / 0.42 ( 12) link_ALPHA1-6 : angle 1.78602 / 1.14 ( 36) link_BETA1-4 : bond 0.00586 / 0.38 ( 20) link_BETA1-4 : angle 2.07927 / 1.30 ( 60) link_NAG-ASN : bond 0.00416 / 0.24 ( 19) link_NAG-ASN : angle 2.43037 / 1.51 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 243 GLN cc_start: 0.7710 (mt0) cc_final: 0.7368 (mp10) REVERT: AAA 250 MET cc_start: 0.7794 (tpp) cc_final: 0.7480 (mmm) REVERT: AAA 253 ASN cc_start: 0.7284 (m-40) cc_final: 0.6987 (m-40) REVERT: AAA 288 VAL cc_start: 0.8313 (t) cc_final: 0.7992 (p) REVERT: AAA 314 SER cc_start: 0.7756 (m) cc_final: 0.7388 (p) REVERT: AAA 316 ASN cc_start: 0.8253 (p0) cc_final: 0.7852 (p0) REVERT: AAA 334 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7414 (mt-10) REVERT: AAA 389 VAL cc_start: 0.7932 (t) cc_final: 0.7472 (m) REVERT: AAA 426 THR cc_start: 0.8227 (p) cc_final: 0.7986 (t) REVERT: AAA 444 VAL cc_start: 0.8766 (t) cc_final: 0.8447 (p) REVERT: AAA 452 ASN cc_start: 0.7702 (m-40) cc_final: 0.7379 (m-40) REVERT: AAA 478 SER cc_start: 0.8401 (m) cc_final: 0.7999 (p) REVERT: AAA 498 THR cc_start: 0.7188 (t) cc_final: 0.6878 (p) REVERT: AAA 520 LEU cc_start: 0.7940 (mm) cc_final: 0.7595 (mm) REVERT: AAA 541 TYR cc_start: 0.6903 (m-10) cc_final: 0.6496 (m-10) REVERT: AAA 550 MET cc_start: 0.6735 (ttt) cc_final: 0.6257 (ttt) REVERT: AAA 575 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6560 (tpp) REVERT: AAA 584 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7527 (tm-30) REVERT: AAA 630 LEU cc_start: 0.8557 (mt) cc_final: 0.8256 (mm) REVERT: AAA 636 SER cc_start: 0.8257 (p) cc_final: 0.8053 (m) REVERT: AAA 660 VAL cc_start: 0.7891 (t) cc_final: 0.7588 (p) REVERT: AAA 683 THR cc_start: 0.8273 (m) cc_final: 0.7942 (p) REVERT: AAA 706 LEU cc_start: 0.7514 (mt) cc_final: 0.7131 (mp) REVERT: AAA 714 ASN cc_start: 0.6961 (m-40) cc_final: 0.6556 (t0) REVERT: AAA 797 SER cc_start: 0.8335 (t) cc_final: 0.7716 (p) REVERT: AAA 798 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (mp) REVERT: AAA 828 SER cc_start: 0.8661 (m) cc_final: 0.7648 (p) REVERT: AAA 833 MET cc_start: 0.6462 (mmm) cc_final: 0.6091 (mmp) REVERT: AAA 859 ASN cc_start: 0.7401 (t0) cc_final: 0.6916 (t0) REVERT: AAA 872 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8309 (p) REVERT: AAA 883 ILE cc_start: 0.8458 (mt) cc_final: 0.8195 (mm) REVERT: AAA 920 TYR cc_start: 0.8038 (p90) cc_final: 0.7668 (p90) REVERT: AAA 939 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6855 (tm-30) outliers start: 39 outliers final: 27 residues processed: 277 average time/residue: 0.0669 time to fit residues: 28.4035 Evaluate side-chains 268 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 34 VAL Chi-restraints excluded: chain AAA residue 61 VAL Chi-restraints excluded: chain AAA residue 176 THR Chi-restraints excluded: chain AAA residue 236 ILE Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 361 ILE Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 611 GLN Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 793 MET Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 806 SER Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.128982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099565 restraints weight = 17662.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103534 restraints weight = 9989.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106213 restraints weight = 6774.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107908 restraints weight = 5190.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109181 restraints weight = 4329.592| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8992 Z= 0.128 Angle : 0.765 12.411 12502 Z= 0.350 Chirality : 0.048 0.432 1669 Planarity : 0.005 0.065 1435 Dihedral : 5.322 29.666 1157 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.13 % Allowed : 22.77 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1038 helix: -1.62 (0.52), residues: 83 sheet: 0.42 (0.25), residues: 431 loop : -1.10 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGAAA 103 TYR 0.016 0.001 TYRAAA 687 PHE 0.024 0.002 PHEAAA1006 TRP 0.043 0.003 TRPAAA 433 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 8923) covalent geometry : angle 0.73425 / 0.34 (12296) SS BOND : bond 0.00483 / 0.25 ( 1) SS BOND : angle 3.35489 / 1.79 ( 2) hydrogen bonds : bond 0.03409 / 2.32 ( 156) hydrogen bonds : angle 5.77737 / 4.05 ( 378) glycosidic custom : bond 0.00146 / 0.11 ( 12) glycosidic custom : angle 1.30344 / 0.83 ( 36) link_ALPHA1-4 : bond 0.00707 / 0.42 ( 5) link_ALPHA1-4 : angle 1.47296 / 0.82 ( 15) link_ALPHA1-6 : bond 0.00555 / 0.35 ( 12) link_ALPHA1-6 : angle 1.72979 / 1.11 ( 36) link_BETA1-4 : bond 0.00533 / 0.35 ( 20) link_BETA1-4 : angle 1.93768 / 1.22 ( 60) link_NAG-ASN : bond 0.00403 / 0.23 ( 19) link_NAG-ASN : angle 2.01766 / 1.26 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 243 GLN cc_start: 0.7609 (mt0) cc_final: 0.7342 (mp10) REVERT: AAA 253 ASN cc_start: 0.7198 (m-40) cc_final: 0.6875 (m-40) REVERT: AAA 288 VAL cc_start: 0.8307 (t) cc_final: 0.7988 (p) REVERT: AAA 316 ASN cc_start: 0.8242 (p0) cc_final: 0.7860 (p0) REVERT: AAA 334 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7397 (mt-10) REVERT: AAA 389 VAL cc_start: 0.7994 (t) cc_final: 0.7573 (m) REVERT: AAA 426 THR cc_start: 0.8178 (p) cc_final: 0.7915 (t) REVERT: AAA 444 VAL cc_start: 0.8757 (t) cc_final: 0.8471 (p) REVERT: AAA 452 ASN cc_start: 0.7671 (m-40) cc_final: 0.7341 (m-40) REVERT: AAA 478 SER cc_start: 0.8431 (m) cc_final: 0.7980 (p) REVERT: AAA 498 THR cc_start: 0.7303 (t) cc_final: 0.6985 (p) REVERT: AAA 520 LEU cc_start: 0.7945 (mm) cc_final: 0.7550 (mm) REVERT: AAA 541 TYR cc_start: 0.6720 (m-10) cc_final: 0.6501 (m-10) REVERT: AAA 550 MET cc_start: 0.6799 (ttt) cc_final: 0.6599 (ttt) REVERT: AAA 575 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6552 (tpp) REVERT: AAA 584 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7639 (tm-30) REVERT: AAA 616 THR cc_start: 0.8238 (p) cc_final: 0.7912 (t) REVERT: AAA 630 LEU cc_start: 0.8555 (mt) cc_final: 0.8271 (mm) REVERT: AAA 636 SER cc_start: 0.8218 (p) cc_final: 0.8017 (m) REVERT: AAA 660 VAL cc_start: 0.7833 (t) cc_final: 0.7518 (p) REVERT: AAA 683 THR cc_start: 0.8109 (m) cc_final: 0.7820 (p) REVERT: AAA 714 ASN cc_start: 0.7025 (m-40) cc_final: 0.6606 (t0) REVERT: AAA 726 VAL cc_start: 0.7845 (t) cc_final: 0.7491 (p) REVERT: AAA 767 TYR cc_start: 0.8678 (m-80) cc_final: 0.8471 (m-80) REVERT: AAA 797 SER cc_start: 0.8329 (t) cc_final: 0.7676 (p) REVERT: AAA 798 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7969 (mp) REVERT: AAA 828 SER cc_start: 0.8602 (m) cc_final: 0.7580 (p) REVERT: AAA 859 ASN cc_start: 0.7320 (t0) cc_final: 0.6827 (t0) REVERT: AAA 872 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8245 (p) REVERT: AAA 883 ILE cc_start: 0.8415 (mt) cc_final: 0.8107 (mm) REVERT: AAA 920 TYR cc_start: 0.8081 (p90) cc_final: 0.7768 (p90) REVERT: AAA 939 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6896 (tm-30) outliers start: 37 outliers final: 24 residues processed: 267 average time/residue: 0.0692 time to fit residues: 28.1203 Evaluate side-chains 267 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 34 VAL Chi-restraints excluded: chain AAA residue 61 VAL Chi-restraints excluded: chain AAA residue 176 THR Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 360 THR Chi-restraints excluded: chain AAA residue 413 THR Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 521 THR Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 789 MET Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.127968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098420 restraints weight = 17837.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102374 restraints weight = 10065.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105035 restraints weight = 6830.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106770 restraints weight = 5233.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.108005 restraints weight = 4362.678| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8992 Z= 0.146 Angle : 0.763 10.839 12502 Z= 0.354 Chirality : 0.047 0.303 1669 Planarity : 0.005 0.067 1435 Dihedral : 5.306 28.772 1157 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.35 % Allowed : 22.88 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1038 helix: -1.55 (0.53), residues: 83 sheet: 0.32 (0.25), residues: 428 loop : -1.14 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARGAAA 103 TYR 0.027 0.001 TYRAAA 642 PHE 0.024 0.001 PHEAAA 738 TRP 0.030 0.003 TRPAAA 433 HIS 0.002 0.001 HISAAA 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8923) covalent geometry : angle 0.73591 / 0.35 (12296) SS BOND : bond 0.00578 / 0.30 ( 1) SS BOND : angle 2.58850 / 1.37 ( 2) hydrogen bonds : bond 0.03615 / 2.44 ( 156) hydrogen bonds : angle 5.73489 / 4.05 ( 378) glycosidic custom : bond 0.00125 / 0.08 ( 12) glycosidic custom : angle 1.26558 / 0.72 ( 36) link_ALPHA1-4 : bond 0.00751 / 0.47 ( 5) link_ALPHA1-4 : angle 1.47648 / 0.83 ( 15) link_ALPHA1-6 : bond 0.00505 / 0.32 ( 12) link_ALPHA1-6 : angle 1.70078 / 1.09 ( 36) link_BETA1-4 : bond 0.00460 / 0.30 ( 20) link_BETA1-4 : angle 1.85101 / 1.14 ( 60) link_NAG-ASN : bond 0.00434 / 0.25 ( 19) link_NAG-ASN : angle 1.87576 / 1.16 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 232 TYR cc_start: 0.7545 (p90) cc_final: 0.6835 (p90) REVERT: AAA 243 GLN cc_start: 0.7740 (mt0) cc_final: 0.7397 (mp10) REVERT: AAA 253 ASN cc_start: 0.7257 (m-40) cc_final: 0.6967 (m-40) REVERT: AAA 288 VAL cc_start: 0.8364 (t) cc_final: 0.8047 (p) REVERT: AAA 334 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7443 (mt-10) REVERT: AAA 401 GLN cc_start: 0.7654 (tp40) cc_final: 0.7258 (tm-30) REVERT: AAA 426 THR cc_start: 0.8178 (p) cc_final: 0.7920 (t) REVERT: AAA 444 VAL cc_start: 0.8778 (t) cc_final: 0.8481 (p) REVERT: AAA 452 ASN cc_start: 0.7781 (m-40) cc_final: 0.7456 (m-40) REVERT: AAA 478 SER cc_start: 0.8422 (m) cc_final: 0.7974 (p) REVERT: AAA 498 THR cc_start: 0.7284 (t) cc_final: 0.6991 (p) REVERT: AAA 509 SER cc_start: 0.7925 (t) cc_final: 0.7698 (t) REVERT: AAA 520 LEU cc_start: 0.7995 (mm) cc_final: 0.7699 (mm) REVERT: AAA 541 TYR cc_start: 0.6755 (m-10) cc_final: 0.6551 (m-10) REVERT: AAA 575 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6318 (mtp) REVERT: AAA 615 PHE cc_start: 0.8031 (m-80) cc_final: 0.7695 (m-80) REVERT: AAA 616 THR cc_start: 0.8217 (p) cc_final: 0.7919 (t) REVERT: AAA 630 LEU cc_start: 0.8539 (mt) cc_final: 0.8250 (mm) REVERT: AAA 649 LEU cc_start: 0.8301 (mt) cc_final: 0.8079 (pp) REVERT: AAA 660 VAL cc_start: 0.7854 (t) cc_final: 0.7545 (p) REVERT: AAA 683 THR cc_start: 0.8074 (m) cc_final: 0.7823 (p) REVERT: AAA 714 ASN cc_start: 0.7030 (m-40) cc_final: 0.6588 (t0) REVERT: AAA 726 VAL cc_start: 0.7964 (t) cc_final: 0.7571 (p) REVERT: AAA 797 SER cc_start: 0.8284 (t) cc_final: 0.7667 (p) REVERT: AAA 798 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7990 (mp) REVERT: AAA 828 SER cc_start: 0.8632 (m) cc_final: 0.7638 (p) REVERT: AAA 833 MET cc_start: 0.6408 (mmm) cc_final: 0.5977 (mmp) REVERT: AAA 859 ASN cc_start: 0.7380 (t0) cc_final: 0.6864 (t0) REVERT: AAA 872 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (p) REVERT: AAA 883 ILE cc_start: 0.8477 (mt) cc_final: 0.8169 (mm) REVERT: AAA 920 TYR cc_start: 0.8172 (p90) cc_final: 0.7819 (p90) REVERT: AAA 939 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6925 (tm-30) REVERT: AAA 974 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7385 (mm-40) REVERT: AAA 979 PHE cc_start: 0.8142 (p90) cc_final: 0.7881 (p90) outliers start: 39 outliers final: 29 residues processed: 266 average time/residue: 0.0661 time to fit residues: 27.1205 Evaluate side-chains 262 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 61 VAL Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 360 THR Chi-restraints excluded: chain AAA residue 361 ILE Chi-restraints excluded: chain AAA residue 383 GLU Chi-restraints excluded: chain AAA residue 392 TYR Chi-restraints excluded: chain AAA residue 413 THR Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 521 THR Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 611 GLN Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 750 THR Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 789 MET Chi-restraints excluded: chain AAA residue 793 MET Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.128047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098752 restraints weight = 17696.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102674 restraints weight = 10043.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105278 restraints weight = 6836.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107061 restraints weight = 5242.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108265 restraints weight = 4356.761| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8992 Z= 0.144 Angle : 0.755 10.356 12502 Z= 0.349 Chirality : 0.047 0.274 1669 Planarity : 0.005 0.067 1435 Dihedral : 5.181 28.951 1157 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.35 % Allowed : 23.10 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % 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: -1.01 (0.26), residues: 1038 helix: -1.45 (0.53), residues: 83 sheet: 0.30 (0.25), residues: 416 loop : -1.33 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 103 TYR 0.024 0.001 TYRAAA 642 PHE 0.022 0.001 PHEAAA1006 TRP 0.021 0.003 TRPAAA 433 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8923) covalent geometry : angle 0.72934 / 0.34 (12296) SS BOND : bond 0.00308 / 0.16 ( 1) SS BOND : angle 2.35469 / 1.24 ( 2) hydrogen bonds : bond 0.03490 / 2.34 ( 156) hydrogen bonds : angle 5.75210 / 4.08 ( 378) glycosidic custom : bond 0.00107 / 0.07 ( 12) glycosidic custom : angle 1.21002 / 0.70 ( 36) link_ALPHA1-4 : bond 0.00727 / 0.43 ( 5) link_ALPHA1-4 : angle 1.50622 / 0.85 ( 15) link_ALPHA1-6 : bond 0.00517 / 0.33 ( 12) link_ALPHA1-6 : angle 1.67205 / 1.04 ( 36) link_BETA1-4 : bond 0.00529 / 0.32 ( 20) link_BETA1-4 : angle 1.82057 / 1.13 ( 60) link_NAG-ASN : bond 0.00377 / 0.21 ( 19) link_NAG-ASN : angle 1.80360 / 1.11 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 52 SER cc_start: 0.8383 (t) cc_final: 0.8084 (p) REVERT: AAA 243 GLN cc_start: 0.7747 (mt0) cc_final: 0.7368 (mp10) REVERT: AAA 253 ASN cc_start: 0.7265 (m-40) cc_final: 0.7004 (m-40) REVERT: AAA 288 VAL cc_start: 0.8348 (t) cc_final: 0.8028 (p) REVERT: AAA 316 ASN cc_start: 0.8136 (p0) cc_final: 0.7888 (p0) REVERT: AAA 334 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7443 (mt-10) REVERT: AAA 365 LYS cc_start: 0.8764 (tttt) cc_final: 0.8198 (tptt) REVERT: AAA 401 GLN cc_start: 0.7549 (tp40) cc_final: 0.7159 (tm-30) REVERT: AAA 411 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8158 (mppt) REVERT: AAA 426 THR cc_start: 0.8182 (p) cc_final: 0.7913 (t) REVERT: AAA 444 VAL cc_start: 0.8769 (t) cc_final: 0.8496 (p) REVERT: AAA 452 ASN cc_start: 0.7863 (m-40) cc_final: 0.7522 (m-40) REVERT: AAA 478 SER cc_start: 0.8410 (m) cc_final: 0.7956 (p) REVERT: AAA 498 THR cc_start: 0.7284 (t) cc_final: 0.6970 (p) REVERT: AAA 509 SER cc_start: 0.7925 (t) cc_final: 0.7679 (t) REVERT: AAA 520 LEU cc_start: 0.8076 (mm) cc_final: 0.7823 (mm) REVERT: AAA 575 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6252 (mtp) REVERT: AAA 615 PHE cc_start: 0.8060 (m-80) cc_final: 0.7783 (m-80) REVERT: AAA 616 THR cc_start: 0.8202 (p) cc_final: 0.7915 (t) REVERT: AAA 630 LEU cc_start: 0.8534 (mt) cc_final: 0.8247 (mm) REVERT: AAA 649 LEU cc_start: 0.8249 (mt) cc_final: 0.8039 (pp) REVERT: AAA 660 VAL cc_start: 0.7844 (t) cc_final: 0.7537 (p) REVERT: AAA 683 THR cc_start: 0.8049 (m) cc_final: 0.7795 (p) REVERT: AAA 714 ASN cc_start: 0.7043 (m-40) cc_final: 0.6611 (t0) REVERT: AAA 726 VAL cc_start: 0.8016 (t) cc_final: 0.7632 (p) REVERT: AAA 755 PRO cc_start: 0.8418 (Cg_endo) cc_final: 0.8185 (Cg_exo) REVERT: AAA 797 SER cc_start: 0.8295 (t) cc_final: 0.7672 (p) REVERT: AAA 798 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (mp) REVERT: AAA 828 SER cc_start: 0.8654 (m) cc_final: 0.7663 (p) REVERT: AAA 833 MET cc_start: 0.6532 (mmm) cc_final: 0.6119 (mmp) REVERT: AAA 859 ASN cc_start: 0.7351 (t0) cc_final: 0.6846 (t0) REVERT: AAA 872 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8260 (p) REVERT: AAA 883 ILE cc_start: 0.8473 (mt) cc_final: 0.8192 (mm) REVERT: AAA 900 SER cc_start: 0.8790 (m) cc_final: 0.8586 (p) REVERT: AAA 901 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (t) REVERT: AAA 920 TYR cc_start: 0.8249 (p90) cc_final: 0.7882 (p90) REVERT: AAA 939 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6924 (tm-30) REVERT: AAA 974 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7378 (mm-40) REVERT: AAA 979 PHE cc_start: 0.8136 (p90) cc_final: 0.7905 (p90) REVERT: AAA 1034 LEU cc_start: 0.8489 (mt) cc_final: 0.8039 (pp) outliers start: 39 outliers final: 31 residues processed: 261 average time/residue: 0.0677 time to fit residues: 27.0429 Evaluate side-chains 262 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 61 VAL Chi-restraints excluded: chain AAA residue 144 LYS Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 360 THR Chi-restraints excluded: chain AAA residue 361 ILE Chi-restraints excluded: chain AAA residue 392 TYR Chi-restraints excluded: chain AAA residue 413 THR Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 483 SER Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 521 THR Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 730 SER Chi-restraints excluded: chain AAA residue 740 LYS Chi-restraints excluded: chain AAA residue 747 PHE Chi-restraints excluded: chain AAA residue 750 THR Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 789 MET Chi-restraints excluded: chain AAA residue 793 MET Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 901 THR Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.4380 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.126337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096678 restraints weight = 17686.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100571 restraints weight = 10127.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103143 restraints weight = 6950.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104907 restraints weight = 5377.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106021 restraints weight = 4492.577| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8992 Z= 0.186 Angle : 0.780 9.825 12502 Z= 0.365 Chirality : 0.048 0.248 1669 Planarity : 0.005 0.072 1435 Dihedral : 5.391 30.022 1157 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.91 % Allowed : 24.78 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % 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: -1.18 (0.26), residues: 1038 helix: -1.45 (0.54), residues: 83 sheet: 0.02 (0.24), residues: 435 loop : -1.35 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARGAAA 272 TYR 0.025 0.002 TYRAAA 642 PHE 0.029 0.002 PHEAAA 738 TRP 0.019 0.003 TRPAAA 433 HIS 0.002 0.001 HISAAA 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 8923) covalent geometry : angle 0.75465 / 0.36 (12296) SS BOND : bond 0.00269 / 0.14 ( 1) SS BOND : angle 2.11463 / 1.12 ( 2) hydrogen bonds : bond 0.03933 / 2.61 ( 156) hydrogen bonds : angle 5.90847 / 4.20 ( 378) glycosidic custom : bond 0.00160 / 0.11 ( 12) glycosidic custom : angle 1.26218 / 0.69 ( 36) link_ALPHA1-4 : bond 0.00586 / 0.36 ( 5) link_ALPHA1-4 : angle 1.55142 / 0.86 ( 15) link_ALPHA1-6 : bond 0.00450 / 0.30 ( 12) link_ALPHA1-6 : angle 1.71020 / 1.09 ( 36) link_BETA1-4 : bond 0.00473 / 0.29 ( 20) link_BETA1-4 : angle 1.83490 / 1.12 ( 60) link_NAG-ASN : bond 0.00444 / 0.26 ( 19) link_NAG-ASN : angle 1.87347 / 1.13 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 52 SER cc_start: 0.8349 (t) cc_final: 0.8071 (p) REVERT: AAA 232 TYR cc_start: 0.7575 (p90) cc_final: 0.6901 (p90) REVERT: AAA 243 GLN cc_start: 0.7766 (mt0) cc_final: 0.7529 (mp10) REVERT: AAA 288 VAL cc_start: 0.8345 (t) cc_final: 0.8025 (p) REVERT: AAA 334 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7439 (mt-10) REVERT: AAA 401 GLN cc_start: 0.7580 (tp40) cc_final: 0.7222 (tm-30) REVERT: AAA 426 THR cc_start: 0.8211 (p) cc_final: 0.7967 (t) REVERT: AAA 444 VAL cc_start: 0.8786 (t) cc_final: 0.8503 (p) REVERT: AAA 452 ASN cc_start: 0.7957 (m-40) cc_final: 0.7627 (m-40) REVERT: AAA 478 SER cc_start: 0.8408 (m) cc_final: 0.7954 (p) REVERT: AAA 498 THR cc_start: 0.7285 (t) cc_final: 0.6987 (p) REVERT: AAA 509 SER cc_start: 0.7945 (t) cc_final: 0.7710 (t) REVERT: AAA 520 LEU cc_start: 0.8154 (mm) cc_final: 0.7868 (mm) REVERT: AAA 575 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6316 (mtp) REVERT: AAA 615 PHE cc_start: 0.8084 (m-80) cc_final: 0.7801 (m-80) REVERT: AAA 616 THR cc_start: 0.8214 (p) cc_final: 0.7940 (t) REVERT: AAA 630 LEU cc_start: 0.8520 (mt) cc_final: 0.8233 (mm) REVERT: AAA 660 VAL cc_start: 0.7862 (t) cc_final: 0.7575 (p) REVERT: AAA 683 THR cc_start: 0.8077 (m) cc_final: 0.7804 (p) REVERT: AAA 714 ASN cc_start: 0.7074 (m-40) cc_final: 0.6683 (t0) REVERT: AAA 726 VAL cc_start: 0.8120 (t) cc_final: 0.7710 (p) REVERT: AAA 755 PRO cc_start: 0.8373 (Cg_endo) cc_final: 0.8105 (Cg_exo) REVERT: AAA 797 SER cc_start: 0.8334 (t) cc_final: 0.7711 (p) REVERT: AAA 798 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (mp) REVERT: AAA 828 SER cc_start: 0.8741 (m) cc_final: 0.8044 (p) REVERT: AAA 833 MET cc_start: 0.6334 (mmm) cc_final: 0.5962 (mmp) REVERT: AAA 859 ASN cc_start: 0.7425 (t0) cc_final: 0.6917 (t0) REVERT: AAA 872 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8320 (p) REVERT: AAA 883 ILE cc_start: 0.8582 (mt) cc_final: 0.8321 (mm) REVERT: AAA 900 SER cc_start: 0.8796 (m) cc_final: 0.8563 (p) REVERT: AAA 920 TYR cc_start: 0.8308 (p90) cc_final: 0.7992 (p90) REVERT: AAA 939 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7096 (tm-30) REVERT: AAA 974 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7397 (mm-40) REVERT: AAA 1034 LEU cc_start: 0.8574 (mt) cc_final: 0.8157 (pp) outliers start: 35 outliers final: 27 residues processed: 261 average time/residue: 0.0695 time to fit residues: 27.7859 Evaluate side-chains 263 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 34 VAL Chi-restraints excluded: chain AAA residue 144 LYS Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 360 THR Chi-restraints excluded: chain AAA residue 361 ILE Chi-restraints excluded: chain AAA residue 391 GLU Chi-restraints excluded: chain AAA residue 413 THR Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 465 GLU Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 730 SER Chi-restraints excluded: chain AAA residue 740 LYS Chi-restraints excluded: chain AAA residue 750 THR Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.128367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099230 restraints weight = 17680.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103100 restraints weight = 10117.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105708 restraints weight = 6923.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107390 restraints weight = 5319.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.108645 restraints weight = 4439.614| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8992 Z= 0.135 Angle : 0.766 9.969 12502 Z= 0.355 Chirality : 0.047 0.242 1669 Planarity : 0.005 0.066 1435 Dihedral : 5.207 30.200 1157 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.57 % Allowed : 26.23 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % 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: -1.10 (0.26), residues: 1038 helix: -1.41 (0.53), residues: 83 sheet: 0.14 (0.25), residues: 421 loop : -1.33 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 103 TYR 0.025 0.001 TYRAAA 642 PHE 0.027 0.002 PHEAAA 738 TRP 0.019 0.003 TRPAAA 960 HIS 0.002 0.001 HISAAA1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8923) covalent geometry : angle 0.74227 / 0.35 (12296) SS BOND : bond 0.00115 / 0.06 ( 1) SS BOND : angle 3.06105 / 1.62 ( 2) hydrogen bonds : bond 0.03450 / 2.33 ( 156) hydrogen bonds : angle 5.85971 / 4.12 ( 378) glycosidic custom : bond 0.00082 / 0.05 ( 12) glycosidic custom : angle 1.13812 / 0.64 ( 36) link_ALPHA1-4 : bond 0.00670 / 0.40 ( 5) link_ALPHA1-4 : angle 1.46036 / 0.81 ( 15) link_ALPHA1-6 : bond 0.00509 / 0.33 ( 12) link_ALPHA1-6 : angle 1.63277 / 1.03 ( 36) link_BETA1-4 : bond 0.00505 / 0.32 ( 20) link_BETA1-4 : angle 1.78628 / 1.12 ( 60) link_NAG-ASN : bond 0.00388 / 0.22 ( 19) link_NAG-ASN : angle 1.72688 / 1.04 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 52 SER cc_start: 0.8352 (t) cc_final: 0.8117 (p) REVERT: AAA 232 TYR cc_start: 0.7545 (p90) cc_final: 0.6913 (p90) REVERT: AAA 243 GLN cc_start: 0.7749 (mt0) cc_final: 0.7529 (mp10) REVERT: AAA 288 VAL cc_start: 0.8346 (t) cc_final: 0.8021 (p) REVERT: AAA 293 GLN cc_start: 0.7225 (tt0) cc_final: 0.6978 (tp40) REVERT: AAA 316 ASN cc_start: 0.8177 (p0) cc_final: 0.7930 (p0) REVERT: AAA 334 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7501 (mt-10) REVERT: AAA 383 GLU cc_start: 0.5766 (pt0) cc_final: 0.5551 (pt0) REVERT: AAA 401 GLN cc_start: 0.7513 (tp40) cc_final: 0.7163 (tm-30) REVERT: AAA 411 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8100 (mtmm) REVERT: AAA 426 THR cc_start: 0.8176 (p) cc_final: 0.7930 (t) REVERT: AAA 444 VAL cc_start: 0.8782 (t) cc_final: 0.8500 (p) REVERT: AAA 452 ASN cc_start: 0.7904 (m-40) cc_final: 0.7549 (m-40) REVERT: AAA 478 SER cc_start: 0.8427 (m) cc_final: 0.7953 (p) REVERT: AAA 498 THR cc_start: 0.7307 (t) cc_final: 0.6969 (p) REVERT: AAA 520 LEU cc_start: 0.8175 (mm) cc_final: 0.7884 (mm) REVERT: AAA 575 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6238 (mtp) REVERT: AAA 615 PHE cc_start: 0.8073 (m-80) cc_final: 0.7752 (m-80) REVERT: AAA 616 THR cc_start: 0.8168 (p) cc_final: 0.7887 (t) REVERT: AAA 630 LEU cc_start: 0.8489 (mt) cc_final: 0.8206 (mm) REVERT: AAA 638 THR cc_start: 0.8572 (m) cc_final: 0.8190 (p) REVERT: AAA 660 VAL cc_start: 0.7838 (t) cc_final: 0.7532 (p) REVERT: AAA 683 THR cc_start: 0.8018 (m) cc_final: 0.7779 (p) REVERT: AAA 714 ASN cc_start: 0.7078 (m-40) cc_final: 0.6704 (t0) REVERT: AAA 721 PHE cc_start: 0.8500 (m-80) cc_final: 0.8134 (m-10) REVERT: AAA 726 VAL cc_start: 0.8061 (t) cc_final: 0.7711 (p) REVERT: AAA 755 PRO cc_start: 0.8367 (Cg_endo) cc_final: 0.8095 (Cg_exo) REVERT: AAA 789 MET cc_start: 0.7854 (ttm) cc_final: 0.7646 (ttm) REVERT: AAA 797 SER cc_start: 0.8309 (t) cc_final: 0.7608 (p) REVERT: AAA 798 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7954 (mp) REVERT: AAA 828 SER cc_start: 0.8398 (m) cc_final: 0.7911 (p) REVERT: AAA 833 MET cc_start: 0.6448 (mmm) cc_final: 0.6048 (mmp) REVERT: AAA 859 ASN cc_start: 0.7292 (t0) cc_final: 0.6777 (t0) REVERT: AAA 872 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8267 (p) REVERT: AAA 883 ILE cc_start: 0.8481 (mt) cc_final: 0.8279 (mm) REVERT: AAA 900 SER cc_start: 0.8864 (m) cc_final: 0.8635 (p) REVERT: AAA 920 TYR cc_start: 0.8308 (p90) cc_final: 0.8044 (p90) REVERT: AAA 939 GLU cc_start: 0.7649 (tm-30) cc_final: 0.6931 (tm-30) REVERT: AAA 960 TRP cc_start: 0.7950 (t60) cc_final: 0.7595 (t60) REVERT: AAA 974 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7373 (mm-40) REVERT: AAA 1034 LEU cc_start: 0.8508 (mt) cc_final: 0.8115 (pp) outliers start: 32 outliers final: 25 residues processed: 259 average time/residue: 0.0694 time to fit residues: 27.4334 Evaluate side-chains 256 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 31 THR Chi-restraints excluded: chain AAA residue 34 VAL Chi-restraints excluded: chain AAA residue 144 LYS Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 258 SER Chi-restraints excluded: chain AAA residue 302 LEU Chi-restraints excluded: chain AAA residue 323 THR Chi-restraints excluded: chain AAA residue 360 THR Chi-restraints excluded: chain AAA residue 391 GLU Chi-restraints excluded: chain AAA residue 413 THR Chi-restraints excluded: chain AAA residue 439 THR Chi-restraints excluded: chain AAA residue 465 GLU Chi-restraints excluded: chain AAA residue 483 SER Chi-restraints excluded: chain AAA residue 492 THR Chi-restraints excluded: chain AAA residue 548 THR Chi-restraints excluded: chain AAA residue 575 MET Chi-restraints excluded: chain AAA residue 651 VAL Chi-restraints excluded: chain AAA residue 667 THR Chi-restraints excluded: chain AAA residue 685 THR Chi-restraints excluded: chain AAA residue 720 ILE Chi-restraints excluded: chain AAA residue 750 THR Chi-restraints excluded: chain AAA residue 785 THR Chi-restraints excluded: chain AAA residue 798 ILE Chi-restraints excluded: chain AAA residue 820 LEU Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 875 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 964 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.124059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095088 restraints weight = 17715.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098866 restraints weight = 10168.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101426 restraints weight = 7002.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103140 restraints weight = 5416.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.104272 restraints weight = 4530.383| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8992 Z= 0.215 Angle : 0.813 9.365 12502 Z= 0.382 Chirality : 0.049 0.238 1669 Planarity : 0.006 0.075 1435 Dihedral : 5.547 32.288 1157 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.68 % Allowed : 26.56 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % 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: -1.32 (0.26), residues: 1038 helix: -1.35 (0.55), residues: 83 sheet: -0.02 (0.25), residues: 431 loop : -1.54 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGAAA 272 TYR 0.027 0.002 TYRAAA 871 PHE 0.032 0.002 PHEAAA 738 TRP 0.017 0.004 TRPAAA 960 HIS 0.002 0.001 HISAAA 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 ( 8923) covalent geometry : angle 0.78774 / 0.38 (12296) SS BOND : bond 0.00468 / 0.25 ( 1) SS BOND : angle 2.73918 / 1.45 ( 2) hydrogen bonds : bond 0.04276 / 2.84 ( 156) hydrogen bonds : angle 6.06255 / 4.29 ( 378) glycosidic custom : bond 0.00217 / 0.15 ( 12) glycosidic custom : angle 1.32786 / 0.72 ( 36) link_ALPHA1-4 : bond 0.00520 / 0.32 ( 5) link_ALPHA1-4 : angle 1.63701 / 0.91 ( 15) link_ALPHA1-6 : bond 0.00413 / 0.28 ( 12) link_ALPHA1-6 : angle 1.70985 / 1.08 ( 36) link_BETA1-4 : bond 0.00432 / 0.27 ( 20) link_BETA1-4 : angle 1.82768 / 1.12 ( 60) link_NAG-ASN : bond 0.00496 / 0.29 ( 19) link_NAG-ASN : angle 1.91169 / 1.17 ( 57) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1656.58 seconds wall clock time: 29 minutes 8.16 seconds (1748.16 seconds total)