Starting phenix.real_space_refine on Thu Jul 2 15:58:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8an2_15530/07_2026/8an2_15530.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 26 5.16 5 C 5495 2.51 5 N 1237 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 8657 Number of models: 1 Model: "" Number of chains: 18 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: 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: "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: 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: "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: 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: "G" 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: "H" 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: "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: 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: "K" 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AAA" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.28, per 1000 atoms: 0.15 Number of scatterers: 8657 At special positions: 0 Unit cell: (158.1, 74.834, 139.128, 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 26 16.00 O 1899 8.00 N 1237 7.00 C 5495 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 D 2 " - " YZT D 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 J 2 " - " YZT J 3 " " NAG K 2 " - " YZT K 3 " " NAG L 2 " - " YZT L 3 " " NAG N 2 " - " YZT N 3 " ALPHA1-4 " NAG B 2 " - " MAN B 5 " " NAG F 2 " - " MAN F 4 " " NAG G 2 " - " MAN G 4 " " NAG J 2 " - " MAN J 4 " " NAG K 2 " - " MAN K 4 " " NAG L 2 " - " MAN L 4 " " NAG N 2 " - " MAN N 4 " ALPHA1-6 " NAG B 2 " - " MAN B 6 " " NAG F 2 " - " MAN F 5 " " NAG G 2 " - " MAN G 5 " " NAG I 2 " - " MAN I 4 " " NAG J 2 " - " MAN J 5 " " NAG K 2 " - " MAN K 5 " " NAG L 2 " - " MAN L 5 " " NAG N 2 " - " MAN N 5 " " NAGBBB 2 " - " MANBBB 3 " 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 " " 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 " " 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 633 " " NAG K 1 " - " ASNAAA 714 " " NAG L 1 " - " ASNAAA 875 " " NAG M 1 " - " ASNAAA 914 " " NAG N 1 " - " ASNAAA 989 " " NAG O 1 " - " ASNAAA1018 " " NAGAAA1509 " - " ASNAAA 559 " " NAGAAA1510 " - " ASNAAA 581 " " NAGAAA1514 " - " ASNAAA 955 " " NAGBBB 1 " - " ASNAAA 60 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 198.2 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 12.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'AAA' and resid 61 through 64 Processing helix chain 'AAA' and resid 70 through 80 removed outlier: 3.641A pdb=" N VALAAA 74 " --> pdb=" O ASNAAA 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SERAAA 80 " --> pdb=" O SERAAA 76 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 138 through 144 removed outlier: 3.746A pdb=" N LYSAAA 144 " --> pdb=" O SERAAA 140 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 147 through 152 Processing helix chain 'AAA' and resid 156 through 160 removed outlier: 4.573A pdb=" N ALAAAA 160 " --> pdb=" O GLUAAA 157 " (cutoff:3.500A) 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 202 removed outlier: 3.550A pdb=" N GLNAAA 198 " --> pdb=" O SERAAA 194 " (cutoff:3.500A) removed outlier: 5.243A 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 263 removed outlier: 4.032A pdb=" N LEUAAA 259 " --> pdb=" O LEUAAA 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALAAAA 263 " --> pdb=" O SERAAA 260 " (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 Processing helix chain 'AAA' and resid 671 through 676 removed outlier: 3.621A pdb=" N ASNAAA 674 " --> pdb=" O ASNAAA 671 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 689 through 692 Processing helix chain 'AAA' and resid 764 through 768 removed outlier: 3.547A pdb=" N LEUAAA 768 " --> pdb=" O THRAAA 765 " (cutoff:3.500A) Processing helix chain 'AAA' and resid 778 through 782 Processing helix chain 'AAA' and resid 874 through 878 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 Processing helix chain 'AAA' and resid 1026 through 1034 removed outlier: 3.791A 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 59 current: chain 'AAA' and resid 119 through 125 removed outlier: 8.819A pdb=" N THRAAA 168 " --> pdb=" O PHEAAA 121 " (cutoff:3.500A) removed outlier: 6.649A 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: 8.306A pdb=" N ILEAAA 82 " --> pdb=" O ARGAAA 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARGAAA 103 " --> pdb=" O ILEAAA 82 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILEAAA 84 " --> pdb=" O THRAAA 101 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THRAAA 101 " --> pdb=" O ILEAAA 84 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALAAAA 86 " --> pdb=" O SERAAA 99 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SERAAA 99 " --> pdb=" O ALAAAA 86 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THRAAA 88 " --> pdb=" O THRAAA 97 " (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 137 removed outlier: 3.782A 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 336 through 341 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 490 through 503 removed outlier: 5.627A pdb=" N ALAAAA 508 " --> pdb=" O ASNAAA 524 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASNAAA 524 " --> pdb=" O ALAAAA 508 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALAAAA 510 " --> pdb=" O TYRAAA 522 " (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 548 through 560 removed outlier: 3.628A pdb=" N VALAAA 553 " --> pdb=" O SERAAA 571 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 581 through 584 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 321 through 324 Processing sheet with id=AA7, first strand: chain 'AAA' and resid 346 through 348 Processing sheet with id=AA8, first strand: chain 'AAA' and resid 389 through 393 Processing sheet with id=AA9, first strand: chain 'AAA' and resid 664 through 667 removed outlier: 8.916A pdb=" N LEUAAA 869 " --> pdb=" O ASNAAA 839 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASNAAA 841 " --> pdb=" O LEUAAA 869 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N TYRAAA 871 " --> pdb=" O ASNAAA 841 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYRAAA 843 " --> pdb=" O TYRAAA 871 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THRAAA 868 " --> pdb=" O ALAAAA 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AAA' and resid 725 through 726 removed outlier: 4.164A pdb=" N THRAAA 745 " --> pdb=" O VALAAA 726 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AAA' and resid 729 through 730 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: 3.690A 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: 7.666A pdb=" N SERAAA 958 " --> pdb=" O LEUAAA 977 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEUAAA 977 " --> pdb=" O SERAAA 958 " (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 1020 through 1025 WARNING: can't find start of bonding for strands! previous: chain 'AAA' and resid 1020 through 1025 current: chain 'AAA' and resid 1058 through 1066 Processing sheet with id=AB8, first strand: chain 'AAA' and resid 966 through 967 158 hydrogen bonds defined for protein. 381 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: 1.49 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1463 1.33 - 1.46: 2833 1.46 - 1.58: 4519 1.58 - 1.71: 5 1.71 - 1.83: 39 Bond restraints: 8859 Sorted by residual: bond pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 1.403 1.529 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " ideal model delta sigma weight residual 1.524 1.620 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.500 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" S6 YZT B 3 " pdb="O1S6 YZT B 3 " ideal model delta sigma weight residual 1.477 1.562 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" S6 YZT I 3 " pdb="O3S6 YZT I 3 " ideal model delta sigma weight residual 1.473 1.550 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 8854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 11659 3.90 - 7.80: 502 7.80 - 11.71: 35 11.71 - 15.61: 7 15.61 - 19.51: 4 Bond angle restraints: 12207 Sorted by residual: angle pdb=" C TYRAAA 696 " pdb=" CA TYRAAA 696 " pdb=" CB TYRAAA 696 " ideal model delta sigma weight residual 110.08 101.80 8.28 1.15e+00 7.56e-01 5.18e+01 angle pdb=" C1 MAN N 5 " pdb=" C2 MAN N 5 " pdb=" O2 MAN N 5 " ideal model delta sigma weight residual 106.80 87.29 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" CA ASNAAA1018 " pdb=" CB ASNAAA1018 " pdb=" CG ASNAAA1018 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.45e+01 angle pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 107.29 124.78 -17.49 3.00e+00 1.11e-01 3.40e+01 angle pdb=" CA ASNAAA 581 " pdb=" CB ASNAAA 581 " pdb=" CG ASNAAA 581 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 ... (remaining 12202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 4357 16.86 - 33.72: 288 33.72 - 50.58: 41 50.58 - 67.43: 10 67.43 - 84.29: 10 Dihedral angle restraints: 4706 sinusoidal: 1674 harmonic: 3032 Sorted by residual: dihedral pdb=" C PHEAAA 782 " pdb=" N PHEAAA 782 " pdb=" CA PHEAAA 782 " pdb=" CB PHEAAA 782 " ideal model delta harmonic sigma weight residual -122.60 -137.24 14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" CA GLYAAA 254 " pdb=" C GLYAAA 254 " pdb=" N ASNAAA 255 " pdb=" CA ASNAAA 255 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" C ASNAAA 875 " pdb=" N ASNAAA 875 " pdb=" CA ASNAAA 875 " pdb=" CB ASNAAA 875 " ideal model delta harmonic sigma weight residual -122.60 -136.13 13.53 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 4703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1244 0.140 - 0.279: 357 0.279 - 0.419: 36 0.419 - 0.559: 5 0.559 - 0.698: 3 Chirality restraints: 1645 Sorted by residual: chirality pdb=" C1 MANBBB 3 " pdb=" O6 NAGBBB 2 " pdb=" C2 MANBBB 3 " pdb=" O5 MANBBB 3 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.17e+02 chirality pdb=" C1 MAN L 4 " pdb=" O4 NAG L 2 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 2.04 0.36 2.00e-02 2.50e+03 3.27e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.60e+02 ... (remaining 1642 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAGAAA1510 " -0.306 2.00e-02 2.50e+03 2.69e-01 9.02e+02 pdb=" C7 NAGAAA1510 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAGAAA1510 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAGAAA1510 " 0.478 2.00e-02 2.50e+03 pdb=" O7 NAGAAA1510 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAGBBB 2 " -0.307 2.00e-02 2.50e+03 2.60e-01 8.45e+02 pdb=" C7 NAGBBB 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAGBBB 2 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAGBBB 2 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAGBBB 2 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.309 2.00e-02 2.50e+03 2.58e-01 8.32e+02 pdb=" C7 NAG F 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.195 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.020 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 1 2.15 - 2.84: 2283 2.84 - 3.52: 10909 3.52 - 4.21: 20433 4.21 - 4.90: 32826 Nonbonded interactions: 66452 Sorted by model distance: nonbonded pdb=" OD1 ASNAAA 581 " pdb=" C1 NAGAAA1510 " model vdw 1.460 2.776 nonbonded pdb=" O5 NAG N 2 " pdb=" O6 NAG N 2 " model vdw 2.338 2.432 nonbonded pdb=" O5 NAGBBB 1 " pdb=" O6 NAGBBB 1 " model vdw 2.355 2.432 nonbonded pdb=" OD1 ASNAAA 342 " pdb=" C1 NAG D 1 " model vdw 2.394 2.776 nonbonded pdb=" OD2 ASPAAA 694 " pdb=" O7 NAG B 2 " model vdw 2.417 3.040 ... (remaining 66447 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 'M' selection = chain 'O' } ncs_group { reference = (chain 'BBB' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.740 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 0.126 8923 Z= 0.702 Angle : 1.989 50.450 12398 Z= 1.084 Chirality : 0.125 0.698 1645 Planarity : 0.027 0.269 1433 Dihedral : 12.510 84.292 2787 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 0.89 % Allowed : 3.35 % Favored : 95.76 % Cbeta Deviations : 1.88 % 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 (0.23), residues: 1038 helix: -2.73 (0.38), residues: 77 sheet: 0.28 (0.26), residues: 324 loop : -1.30 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.006 ARGAAA 272 TYR 0.070 0.008 TYRAAA 141 PHE 0.036 0.007 PHEAAA 656 TRP 0.043 0.012 TRPAAA 960 HIS 0.011 0.006 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.01171 / 0.70 ( 8859) covalent geometry : angle 1.86621 / 1.06 (12207) SS BOND : bond 0.02345 / 1.23 ( 1) SS BOND : angle 2.71944 / 1.55 ( 2) hydrogen bonds : bond 0.20996 / 13.66 ( 158) hydrogen bonds : angle 7.53444 / 5.08 ( 381) glycosidic custom : bond 0.01147 / 0.63 ( 11) glycosidic custom : angle 3.51778 / 2.12 ( 33) link_ALPHA1-4 : bond 0.01426 / 0.78 ( 7) link_ALPHA1-4 : angle 3.17544 / 2.03 ( 21) link_ALPHA1-6 : bond 0.02109 / 1.43 ( 9) link_ALPHA1-6 : angle 3.75340 / 2.31 ( 27) link_BETA1-4 : bond 0.01267 / 0.66 ( 17) link_BETA1-4 : angle 4.41425 / 3.15 ( 51) link_NAG-ASN : bond 0.01782 / 1.10 ( 19) link_NAG-ASN : angle 8.93258 / 4.81 ( 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 209 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 75 ILE cc_start: 0.8249 (pp) cc_final: 0.8016 (mt) REVERT: AAA 79 VAL cc_start: 0.8111 (m) cc_final: 0.7841 (t) REVERT: AAA 103 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8153 (mtp-110) REVERT: AAA 136 ASN cc_start: 0.8767 (p0) cc_final: 0.8518 (m110) REVERT: AAA 141 TYR cc_start: 0.8224 (t80) cc_final: 0.7786 (t80) REVERT: AAA 144 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8914 (mtpt) REVERT: AAA 203 MET cc_start: 0.7857 (mmt) cc_final: 0.7620 (mmt) REVERT: AAA 207 VAL cc_start: 0.8970 (t) cc_final: 0.8737 (m) REVERT: AAA 230 ILE cc_start: 0.8281 (mt) cc_final: 0.8059 (mm) REVERT: AAA 291 THR cc_start: 0.8659 (m) cc_final: 0.8273 (p) REVERT: AAA 427 ILE cc_start: 0.7646 (mt) cc_final: 0.7217 (mt) REVERT: AAA 436 THR cc_start: 0.7711 (m) cc_final: 0.7088 (t) REVERT: AAA 465 GLU cc_start: 0.8503 (tt0) cc_final: 0.8222 (tt0) REVERT: AAA 502 LYS cc_start: 0.7880 (tptt) cc_final: 0.7627 (tptt) REVERT: AAA 712 ASN cc_start: 0.8474 (p0) cc_final: 0.8241 (p0) REVERT: AAA 715 ILE cc_start: 0.8648 (mm) cc_final: 0.8430 (mm) REVERT: AAA 767 TYR cc_start: 0.8038 (m-80) cc_final: 0.7715 (m-80) REVERT: AAA 872 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8257 (t) REVERT: AAA 905 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8062 (mtmt) REVERT: AAA 918 ASN cc_start: 0.8477 (t0) cc_final: 0.8258 (m-40) REVERT: AAA 942 TYR cc_start: 0.8772 (m-10) cc_final: 0.8503 (m-10) REVERT: AAA 950 ILE cc_start: 0.7916 (mt) cc_final: 0.7640 (tt) REVERT: AAA 962 SER cc_start: 0.8075 (t) cc_final: 0.7847 (p) REVERT: AAA 1012 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7921 (mp10) REVERT: AAA 1015 GLN cc_start: 0.7981 (mt0) cc_final: 0.7771 (mp10) REVERT: AAA 1022 GLN cc_start: 0.8248 (tt0) cc_final: 0.8024 (tm-30) outliers start: 8 outliers final: 4 residues processed: 208 average time/residue: 0.0533 time to fit residues: 16.8784 Evaluate side-chains 160 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 100 VAL Chi-restraints excluded: chain AAA residue 256 LEU Chi-restraints excluded: chain AAA residue 426 THR Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 872 VAL 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: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.142333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107029 restraints weight = 14219.522| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.49 r_work: 0.3228 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8923 Z= 0.193 Angle : 0.921 10.856 12398 Z= 0.415 Chirality : 0.052 0.517 1645 Planarity : 0.006 0.052 1433 Dihedral : 6.839 49.603 1157 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.90 % Allowed : 10.16 % Favored : 86.94 % 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 (0.24), residues: 1038 helix: -2.14 (0.38), residues: 104 sheet: 0.54 (0.26), residues: 342 loop : -1.14 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARGAAA 103 TYR 0.017 0.002 TYRAAA 843 PHE 0.017 0.002 PHEAAA 215 TRP 0.020 0.003 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 8859) covalent geometry : angle 0.85705 / 0.40 (12207) SS BOND : bond 0.00645 / 0.34 ( 1) SS BOND : angle 2.04368 / 1.13 ( 2) hydrogen bonds : bond 0.04663 / 3.17 ( 158) hydrogen bonds : angle 5.56776 / 3.68 ( 381) glycosidic custom : bond 0.00360 / 0.22 ( 11) glycosidic custom : angle 2.31753 / 1.50 ( 33) link_ALPHA1-4 : bond 0.00896 / 0.51 ( 7) link_ALPHA1-4 : angle 1.61408 / 1.09 ( 21) link_ALPHA1-6 : bond 0.00638 / 0.35 ( 9) link_ALPHA1-6 : angle 1.91931 / 1.11 ( 27) link_BETA1-4 : bond 0.00917 / 0.48 ( 17) link_BETA1-4 : angle 2.56338 / 1.65 ( 51) link_NAG-ASN : bond 0.00557 / 0.33 ( 19) link_NAG-ASN : angle 3.92017 / 2.42 ( 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 189 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.209 Fit side-chains REVERT: AAA 75 ILE cc_start: 0.7894 (pp) cc_final: 0.7661 (mt) REVERT: AAA 82 ILE cc_start: 0.8222 (mt) cc_final: 0.7869 (mp) REVERT: AAA 110 ASN cc_start: 0.7035 (m110) cc_final: 0.6824 (m-40) REVERT: AAA 141 TYR cc_start: 0.7468 (t80) cc_final: 0.7244 (t80) REVERT: AAA 144 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8247 (mtpt) REVERT: AAA 207 VAL cc_start: 0.8682 (t) cc_final: 0.8439 (m) REVERT: AAA 230 ILE cc_start: 0.7801 (mt) cc_final: 0.7507 (mm) REVERT: AAA 452 ASN cc_start: 0.7831 (p0) cc_final: 0.7629 (p0) REVERT: AAA 460 LYS cc_start: 0.8209 (pttt) cc_final: 0.7777 (mtpp) REVERT: AAA 473 GLN cc_start: 0.7374 (tm-30) cc_final: 0.7085 (tm-30) REVERT: AAA 492 THR cc_start: 0.8072 (p) cc_final: 0.7683 (t) REVERT: AAA 524 ASN cc_start: 0.6690 (p0) cc_final: 0.6351 (p0) REVERT: AAA 706 LEU cc_start: 0.7457 (mt) cc_final: 0.7242 (mp) REVERT: AAA 712 ASN cc_start: 0.7683 (p0) cc_final: 0.7454 (p0) REVERT: AAA 715 ILE cc_start: 0.8262 (mm) cc_final: 0.7976 (mm) REVERT: AAA 872 VAL cc_start: 0.8158 (m) cc_final: 0.7858 (t) REVERT: AAA 905 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7432 (mtmt) REVERT: AAA 950 ILE cc_start: 0.7466 (mt) cc_final: 0.7174 (tt) REVERT: AAA 979 PHE cc_start: 0.7547 (p90) cc_final: 0.7334 (p90) REVERT: AAA 1005 LEU cc_start: 0.8284 (mt) cc_final: 0.8053 (mm) outliers start: 26 outliers final: 19 residues processed: 175 average time/residue: 0.0610 time to fit residues: 15.9423 Evaluate side-chains 172 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 84 ILE Chi-restraints excluded: chain AAA residue 100 VAL Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 385 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 531 SER Chi-restraints excluded: chain AAA residue 634 LEU Chi-restraints excluded: chain AAA residue 666 SER Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 713 MET Chi-restraints excluded: chain AAA residue 739 ASN Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 916 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.140703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106012 restraints weight = 14064.830| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.10 r_work: 0.3222 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8923 Z= 0.219 Angle : 0.863 12.266 12398 Z= 0.395 Chirality : 0.050 0.385 1645 Planarity : 0.006 0.057 1433 Dihedral : 6.256 41.350 1153 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.79 % Allowed : 10.83 % Favored : 85.38 % 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 (0.24), residues: 1038 helix: -1.86 (0.43), residues: 104 sheet: 0.40 (0.25), residues: 392 loop : -1.10 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 103 TYR 0.020 0.002 TYRAAA 672 PHE 0.018 0.002 PHEAAA 336 TRP 0.017 0.003 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 8859) covalent geometry : angle 0.80597 / 0.38 (12207) SS BOND : bond 0.00708 / 0.37 ( 1) SS BOND : angle 2.38800 / 1.30 ( 2) hydrogen bonds : bond 0.04454 / 3.02 ( 158) hydrogen bonds : angle 5.23323 / 3.44 ( 381) glycosidic custom : bond 0.00228 / 0.12 ( 11) glycosidic custom : angle 2.05427 / 1.37 ( 33) link_ALPHA1-4 : bond 0.00779 / 0.45 ( 7) link_ALPHA1-4 : angle 1.77482 / 1.11 ( 21) link_ALPHA1-6 : bond 0.00563 / 0.31 ( 9) link_ALPHA1-6 : angle 1.74442 / 1.01 ( 27) link_BETA1-4 : bond 0.00737 / 0.42 ( 17) link_BETA1-4 : angle 2.46694 / 1.61 ( 51) link_NAG-ASN : bond 0.00490 / 0.27 ( 19) link_NAG-ASN : angle 3.50607 / 2.17 ( 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 203 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.284 Fit side-chains REVERT: AAA 75 ILE cc_start: 0.7931 (pp) cc_final: 0.7666 (mt) REVERT: AAA 82 ILE cc_start: 0.8206 (mt) cc_final: 0.7813 (mp) REVERT: AAA 125 SER cc_start: 0.7733 (p) cc_final: 0.7353 (p) REVERT: AAA 141 TYR cc_start: 0.7635 (t80) cc_final: 0.7377 (t80) REVERT: AAA 144 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8278 (mtpt) REVERT: AAA 191 SER cc_start: 0.8091 (m) cc_final: 0.7813 (p) REVERT: AAA 207 VAL cc_start: 0.8712 (t) cc_final: 0.8471 (m) REVERT: AAA 230 ILE cc_start: 0.7805 (mt) cc_final: 0.7522 (mm) REVERT: AAA 250 MET cc_start: 0.8372 (ttm) cc_final: 0.8172 (ttm) REVERT: AAA 460 LYS cc_start: 0.8221 (pttt) cc_final: 0.7881 (mtpp) REVERT: AAA 531 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7625 (m) REVERT: AAA 712 ASN cc_start: 0.7638 (p0) cc_final: 0.7361 (p0) REVERT: AAA 715 ILE cc_start: 0.8183 (mm) cc_final: 0.7954 (mm) REVERT: AAA 872 VAL cc_start: 0.8096 (m) cc_final: 0.7836 (t) REVERT: AAA 905 LYS cc_start: 0.7700 (mtmt) cc_final: 0.7459 (mtmt) REVERT: AAA 950 ILE cc_start: 0.7428 (mt) cc_final: 0.7163 (tt) REVERT: AAA 1005 LEU cc_start: 0.8305 (mt) cc_final: 0.8051 (mm) REVERT: AAA 1015 GLN cc_start: 0.7205 (mp10) cc_final: 0.6996 (mt0) outliers start: 34 outliers final: 25 residues processed: 187 average time/residue: 0.0586 time to fit residues: 16.5352 Evaluate side-chains 186 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 131 THR Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 385 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 442 ILE Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 531 SER Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 634 LEU Chi-restraints excluded: chain AAA residue 666 SER Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 713 MET Chi-restraints excluded: chain AAA residue 739 ASN Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 859 ASN Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 948 THR Chi-restraints excluded: chain AAA residue 983 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106350 restraints weight = 14296.067| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.50 r_work: 0.3232 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8923 Z= 0.151 Angle : 0.769 10.780 12398 Z= 0.347 Chirality : 0.047 0.335 1645 Planarity : 0.006 0.054 1433 Dihedral : 5.730 42.100 1152 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 13.62 % Favored : 83.37 % 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: -0.71 (0.25), residues: 1038 helix: -1.27 (0.50), residues: 92 sheet: 0.35 (0.24), residues: 421 loop : -0.99 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 272 TYR 0.016 0.001 TYRAAA 672 PHE 0.015 0.002 PHEAAA 215 TRP 0.014 0.002 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8859) covalent geometry : angle 0.71622 / 0.34 (12207) SS BOND : bond 0.00596 / 0.31 ( 1) SS BOND : angle 2.10195 / 1.15 ( 2) hydrogen bonds : bond 0.03651 / 2.49 ( 158) hydrogen bonds : angle 5.00017 / 3.30 ( 381) glycosidic custom : bond 0.00192 / 0.12 ( 11) glycosidic custom : angle 1.73974 / 1.17 ( 33) link_ALPHA1-4 : bond 0.00728 / 0.41 ( 7) link_ALPHA1-4 : angle 1.58709 / 0.99 ( 21) link_ALPHA1-6 : bond 0.00561 / 0.30 ( 9) link_ALPHA1-6 : angle 1.64562 / 0.99 ( 27) link_BETA1-4 : bond 0.00698 / 0.38 ( 17) link_BETA1-4 : angle 2.29306 / 1.43 ( 51) link_NAG-ASN : bond 0.00400 / 0.22 ( 19) link_NAG-ASN : angle 3.14215 / 1.85 ( 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 184 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: AAA 75 ILE cc_start: 0.7980 (pp) cc_final: 0.7717 (mt) REVERT: AAA 82 ILE cc_start: 0.8231 (mt) cc_final: 0.7877 (mp) REVERT: AAA 103 ARG cc_start: 0.7463 (ttp-110) cc_final: 0.7057 (mtp-110) REVERT: AAA 207 VAL cc_start: 0.8727 (t) cc_final: 0.8490 (m) REVERT: AAA 230 ILE cc_start: 0.7790 (mt) cc_final: 0.7508 (mm) REVERT: AAA 262 GLU cc_start: 0.7025 (pt0) cc_final: 0.6804 (pm20) REVERT: AAA 460 LYS cc_start: 0.8269 (pttt) cc_final: 0.7933 (mtpp) REVERT: AAA 712 ASN cc_start: 0.7626 (p0) cc_final: 0.7325 (p0) REVERT: AAA 715 ILE cc_start: 0.8197 (mm) cc_final: 0.7969 (mm) REVERT: AAA 872 VAL cc_start: 0.8041 (m) cc_final: 0.7795 (t) REVERT: AAA 905 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7472 (mtmt) REVERT: AAA 1005 LEU cc_start: 0.8341 (mt) cc_final: 0.8055 (mm) REVERT: AAA 1015 GLN cc_start: 0.7203 (mp10) cc_final: 0.6932 (mp10) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 0.0573 time to fit residues: 14.7510 Evaluate side-chains 171 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 101 THR Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 385 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 634 LEU Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 739 ASN Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 983 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.142018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106435 restraints weight = 14299.302| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.49 r_work: 0.3216 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8923 Z= 0.143 Angle : 0.735 10.338 12398 Z= 0.333 Chirality : 0.046 0.310 1645 Planarity : 0.005 0.050 1433 Dihedral : 5.460 42.353 1152 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.02 % Allowed : 13.17 % Favored : 82.81 % 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: -0.62 (0.25), residues: 1038 helix: -1.04 (0.53), residues: 92 sheet: 0.49 (0.25), residues: 414 loop : -1.01 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGAAA 103 TYR 0.018 0.002 TYRAAA 141 PHE 0.013 0.001 PHEAAA 336 TRP 0.013 0.002 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8859) covalent geometry : angle 0.68694 / 0.32 (12207) SS BOND : bond 0.00565 / 0.30 ( 1) SS BOND : angle 2.08468 / 1.14 ( 2) hydrogen bonds : bond 0.03419 / 2.36 ( 158) hydrogen bonds : angle 4.84337 / 3.21 ( 381) glycosidic custom : bond 0.00153 / 0.10 ( 11) glycosidic custom : angle 1.63000 / 1.08 ( 33) link_ALPHA1-4 : bond 0.00743 / 0.42 ( 7) link_ALPHA1-4 : angle 1.61808 / 1.02 ( 21) link_ALPHA1-6 : bond 0.00547 / 0.29 ( 9) link_ALPHA1-6 : angle 1.60876 / 0.96 ( 27) link_BETA1-4 : bond 0.00644 / 0.35 ( 17) link_BETA1-4 : angle 2.17863 / 1.37 ( 51) link_NAG-ASN : bond 0.00334 / 0.18 ( 19) link_NAG-ASN : angle 2.88082 / 1.71 ( 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 192 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: AAA 75 ILE cc_start: 0.7960 (pp) cc_final: 0.7694 (mt) REVERT: AAA 82 ILE cc_start: 0.8214 (mt) cc_final: 0.7847 (mp) REVERT: AAA 103 ARG cc_start: 0.7414 (ttp-110) cc_final: 0.7128 (mtp180) REVERT: AAA 207 VAL cc_start: 0.8736 (t) cc_final: 0.8513 (m) REVERT: AAA 230 ILE cc_start: 0.7793 (mt) cc_final: 0.7511 (mm) REVERT: AAA 262 GLU cc_start: 0.7031 (pt0) cc_final: 0.6792 (pm20) REVERT: AAA 327 TYR cc_start: 0.7740 (t80) cc_final: 0.7535 (t80) REVERT: AAA 460 LYS cc_start: 0.8278 (pttt) cc_final: 0.7937 (mtpp) REVERT: AAA 573 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7108 (pp20) REVERT: AAA 712 ASN cc_start: 0.7633 (p0) cc_final: 0.7313 (p0) REVERT: AAA 715 ILE cc_start: 0.8190 (mm) cc_final: 0.7952 (mm) REVERT: AAA 872 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7792 (t) REVERT: AAA 905 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7487 (mtmt) REVERT: AAA 1005 LEU cc_start: 0.8360 (mt) cc_final: 0.8045 (mm) REVERT: AAA 1015 GLN cc_start: 0.7239 (mp10) cc_final: 0.6956 (mp10) REVERT: AAA 1022 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7323 (tm-30) outliers start: 36 outliers final: 24 residues processed: 174 average time/residue: 0.0531 time to fit residues: 13.9060 Evaluate side-chains 180 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 101 THR Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 527 LEU Chi-restraints excluded: chain AAA residue 531 SER Chi-restraints excluded: chain AAA residue 573 GLU Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 634 LEU Chi-restraints excluded: chain AAA residue 666 SER Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 713 MET Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 859 ASN Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 1002 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.142032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106771 restraints weight = 14119.565| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.50 r_work: 0.3224 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8923 Z= 0.140 Angle : 0.721 10.653 12398 Z= 0.325 Chirality : 0.046 0.296 1645 Planarity : 0.005 0.049 1433 Dihedral : 5.304 42.887 1152 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.24 % Allowed : 13.84 % Favored : 82.92 % 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: -0.54 (0.25), residues: 1038 helix: -0.69 (0.54), residues: 86 sheet: 0.56 (0.25), residues: 414 loop : -1.03 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGAAA 103 TYR 0.018 0.001 TYRAAA 672 PHE 0.021 0.002 PHEAAA 215 TRP 0.010 0.002 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8859) covalent geometry : angle 0.67226 / 0.31 (12207) SS BOND : bond 0.00521 / 0.27 ( 1) SS BOND : angle 1.98062 / 1.08 ( 2) hydrogen bonds : bond 0.03313 / 2.27 ( 158) hydrogen bonds : angle 4.77932 / 3.18 ( 381) glycosidic custom : bond 0.00139 / 0.09 ( 11) glycosidic custom : angle 1.50682 / 1.00 ( 33) link_ALPHA1-4 : bond 0.00746 / 0.42 ( 7) link_ALPHA1-4 : angle 1.58835 / 0.99 ( 21) link_ALPHA1-6 : bond 0.00537 / 0.29 ( 9) link_ALPHA1-6 : angle 1.59774 / 0.95 ( 27) link_BETA1-4 : bond 0.00715 / 0.36 ( 17) link_BETA1-4 : angle 2.05650 / 1.30 ( 51) link_NAG-ASN : bond 0.00292 / 0.16 ( 19) link_NAG-ASN : angle 2.98517 / 1.75 ( 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 187 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AAA 59 VAL cc_start: 0.8034 (t) cc_final: 0.7636 (m) REVERT: AAA 75 ILE cc_start: 0.7958 (pp) cc_final: 0.7700 (mt) REVERT: AAA 103 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7094 (mtp180) REVERT: AAA 207 VAL cc_start: 0.8719 (t) cc_final: 0.8497 (m) REVERT: AAA 230 ILE cc_start: 0.7772 (mt) cc_final: 0.7492 (mm) REVERT: AAA 460 LYS cc_start: 0.8267 (pttt) cc_final: 0.7923 (mtpp) REVERT: AAA 712 ASN cc_start: 0.7611 (p0) cc_final: 0.7283 (p0) REVERT: AAA 715 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7982 (mm) REVERT: AAA 872 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7789 (t) REVERT: AAA 905 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7473 (mtmt) REVERT: AAA 981 LYS cc_start: 0.7864 (tttm) cc_final: 0.7614 (tttm) REVERT: AAA 1005 LEU cc_start: 0.8392 (mt) cc_final: 0.8140 (mm) outliers start: 29 outliers final: 24 residues processed: 172 average time/residue: 0.0571 time to fit residues: 14.6101 Evaluate side-chains 182 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 101 THR Chi-restraints excluded: chain AAA residue 103 ARG Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 527 LEU Chi-restraints excluded: chain AAA residue 531 SER Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 634 LEU Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 715 ILE Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 1002 MET Chi-restraints excluded: chain AAA residue 1009 LEU Chi-restraints excluded: chain AAA residue 1034 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 0.0040 overall best weight: 0.7754 ------------------------------------------------------------------------------- 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 = 0.142222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107046 restraints weight = 14220.838| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.49 r_work: 0.3224 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8923 Z= 0.147 Angle : 0.723 10.710 12398 Z= 0.329 Chirality : 0.046 0.284 1645 Planarity : 0.005 0.051 1433 Dihedral : 5.240 42.936 1152 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.35 % Allowed : 14.62 % Favored : 82.03 % 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: -0.53 (0.25), residues: 1038 helix: -0.47 (0.56), residues: 86 sheet: 0.54 (0.26), residues: 402 loop : -1.02 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGAAA 272 TYR 0.019 0.002 TYRAAA 672 PHE 0.013 0.002 PHEAAA 290 TRP 0.010 0.002 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8859) covalent geometry : angle 0.67745 / 0.32 (12207) SS BOND : bond 0.00582 / 0.31 ( 1) SS BOND : angle 2.14641 / 1.17 ( 2) hydrogen bonds : bond 0.03376 / 2.29 ( 158) hydrogen bonds : angle 4.76792 / 3.18 ( 381) glycosidic custom : bond 0.00127 / 0.08 ( 11) glycosidic custom : angle 1.50477 / 1.00 ( 33) link_ALPHA1-4 : bond 0.00714 / 0.40 ( 7) link_ALPHA1-4 : angle 1.59501 / 0.99 ( 21) link_ALPHA1-6 : bond 0.00527 / 0.29 ( 9) link_ALPHA1-6 : angle 1.61228 / 0.95 ( 27) link_BETA1-4 : bond 0.00605 / 0.33 ( 17) link_BETA1-4 : angle 2.05567 / 1.28 ( 51) link_NAG-ASN : bond 0.00286 / 0.16 ( 19) link_NAG-ASN : angle 2.85453 / 1.69 ( 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 188 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AAA 59 VAL cc_start: 0.8053 (t) cc_final: 0.7628 (m) REVERT: AAA 75 ILE cc_start: 0.7934 (pp) cc_final: 0.7680 (mt) REVERT: AAA 90 ASN cc_start: 0.7381 (t0) cc_final: 0.7140 (t0) REVERT: AAA 103 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7068 (mtp180) REVERT: AAA 151 THR cc_start: 0.8249 (m) cc_final: 0.7989 (p) REVERT: AAA 207 VAL cc_start: 0.8732 (t) cc_final: 0.8515 (m) REVERT: AAA 230 ILE cc_start: 0.7769 (mt) cc_final: 0.7492 (mm) REVERT: AAA 262 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: AAA 460 LYS cc_start: 0.8337 (pttt) cc_final: 0.7993 (mtpp) REVERT: AAA 573 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7180 (pp20) REVERT: AAA 712 ASN cc_start: 0.7618 (p0) cc_final: 0.7286 (p0) REVERT: AAA 715 ILE cc_start: 0.8262 (mm) cc_final: 0.7988 (mt) REVERT: AAA 872 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7792 (t) REVERT: AAA 905 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7467 (mtmt) REVERT: AAA 920 TYR cc_start: 0.7208 (p90) cc_final: 0.6908 (p90) REVERT: AAA 1005 LEU cc_start: 0.8375 (mt) cc_final: 0.8157 (mm) REVERT: AAA 1015 GLN cc_start: 0.7310 (mp10) cc_final: 0.7106 (mt0) outliers start: 30 outliers final: 25 residues processed: 173 average time/residue: 0.0635 time to fit residues: 16.4016 Evaluate side-chains 189 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 103 ARG Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 190 THR Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 262 GLU Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 449 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 527 LEU Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 573 GLU Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 634 LEU Chi-restraints excluded: chain AAA residue 666 SER Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 713 MET Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 1002 MET Chi-restraints excluded: chain AAA residue 1034 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.142191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108469 restraints weight = 14204.010| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.31 r_work: 0.3229 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8923 Z= 0.120 Angle : 0.689 10.434 12398 Z= 0.312 Chirality : 0.045 0.282 1645 Planarity : 0.005 0.050 1433 Dihedral : 5.027 43.582 1152 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.35 % Allowed : 15.18 % Favored : 81.47 % 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: -0.34 (0.26), residues: 1038 helix: -0.48 (0.56), residues: 86 sheet: 0.63 (0.26), residues: 410 loop : -0.85 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGAAA 272 TYR 0.015 0.001 TYRAAA 672 PHE 0.021 0.001 PHEAAA 215 TRP 0.011 0.001 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8859) covalent geometry : angle 0.64635 / 0.30 (12207) SS BOND : bond 0.00460 / 0.24 ( 1) SS BOND : angle 1.83610 / 1.00 ( 2) hydrogen bonds : bond 0.02992 / 2.03 ( 158) hydrogen bonds : angle 4.66635 / 3.11 ( 381) glycosidic custom : bond 0.00137 / 0.10 ( 11) glycosidic custom : angle 1.37518 / 0.91 ( 33) link_ALPHA1-4 : bond 0.00703 / 0.40 ( 7) link_ALPHA1-4 : angle 1.53497 / 0.95 ( 21) link_ALPHA1-6 : bond 0.00546 / 0.29 ( 9) link_ALPHA1-6 : angle 1.58061 / 0.94 ( 27) link_BETA1-4 : bond 0.00637 / 0.34 ( 17) link_BETA1-4 : angle 1.93403 / 1.19 ( 51) link_NAG-ASN : bond 0.00293 / 0.17 ( 19) link_NAG-ASN : angle 2.66385 / 1.60 ( 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 196 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AAA 59 VAL cc_start: 0.8086 (t) cc_final: 0.7622 (m) REVERT: AAA 75 ILE cc_start: 0.7945 (pp) cc_final: 0.7691 (mt) REVERT: AAA 90 ASN cc_start: 0.7328 (t0) cc_final: 0.7089 (t0) REVERT: AAA 103 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7037 (mtp180) REVERT: AAA 151 THR cc_start: 0.8242 (m) cc_final: 0.7976 (p) REVERT: AAA 207 VAL cc_start: 0.8749 (t) cc_final: 0.8530 (m) REVERT: AAA 230 ILE cc_start: 0.7753 (mt) cc_final: 0.7502 (mm) REVERT: AAA 262 GLU cc_start: 0.6898 (pm20) cc_final: 0.6465 (pm20) REVERT: AAA 326 SER cc_start: 0.8056 (p) cc_final: 0.7743 (m) REVERT: AAA 460 LYS cc_start: 0.8368 (pttt) cc_final: 0.8019 (mtpp) REVERT: AAA 611 GLN cc_start: 0.7676 (mm110) cc_final: 0.7205 (mm-40) REVERT: AAA 712 ASN cc_start: 0.7619 (p0) cc_final: 0.7284 (p0) REVERT: AAA 715 ILE cc_start: 0.8265 (mm) cc_final: 0.7984 (mt) REVERT: AAA 872 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7779 (t) REVERT: AAA 905 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7471 (mtmt) REVERT: AAA 920 TYR cc_start: 0.7215 (p90) cc_final: 0.6863 (p90) REVERT: AAA 936 TYR cc_start: 0.7835 (m-80) cc_final: 0.7544 (m-80) REVERT: AAA 991 THR cc_start: 0.7094 (m) cc_final: 0.6617 (p) REVERT: AAA 1015 GLN cc_start: 0.7299 (mp10) cc_final: 0.6975 (mp10) outliers start: 30 outliers final: 24 residues processed: 182 average time/residue: 0.0627 time to fit residues: 16.9987 Evaluate side-chains 192 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 103 ARG Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 178 THR Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 449 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 527 LEU Chi-restraints excluded: chain AAA residue 535 ILE Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 666 SER Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 713 MET Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 1002 MET Chi-restraints excluded: chain AAA residue 1034 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.0040 chunk 65 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 90 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.2550 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.143190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108805 restraints weight = 14322.832| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.51 r_work: 0.3238 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8923 Z= 0.100 Angle : 0.658 9.902 12398 Z= 0.297 Chirality : 0.044 0.259 1645 Planarity : 0.005 0.050 1433 Dihedral : 4.743 43.710 1152 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.79 % Allowed : 15.74 % Favored : 81.47 % 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: -0.11 (0.26), residues: 1038 helix: -0.39 (0.56), residues: 86 sheet: 0.67 (0.25), residues: 445 loop : -0.66 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARGAAA 272 TYR 0.013 0.001 TYRAAA 672 PHE 0.008 0.001 PHEAAA 614 TRP 0.011 0.001 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 8859) covalent geometry : angle 0.62059 / 0.29 (12207) SS BOND : bond 0.00404 / 0.21 ( 1) SS BOND : angle 1.73939 / 0.95 ( 2) hydrogen bonds : bond 0.02634 / 1.76 ( 158) hydrogen bonds : angle 4.48828 / 2.99 ( 381) glycosidic custom : bond 0.00150 / 0.10 ( 11) glycosidic custom : angle 1.24435 / 0.82 ( 33) link_ALPHA1-4 : bond 0.00709 / 0.40 ( 7) link_ALPHA1-4 : angle 1.49814 / 0.93 ( 21) link_ALPHA1-6 : bond 0.00562 / 0.30 ( 9) link_ALPHA1-6 : angle 1.54992 / 0.93 ( 27) link_BETA1-4 : bond 0.00609 / 0.33 ( 17) link_BETA1-4 : angle 1.79905 / 1.08 ( 51) link_NAG-ASN : bond 0.00288 / 0.17 ( 19) link_NAG-ASN : angle 2.44358 / 1.53 ( 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 191 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 59 VAL cc_start: 0.8137 (t) cc_final: 0.7679 (m) REVERT: AAA 75 ILE cc_start: 0.7925 (pp) cc_final: 0.7668 (mt) REVERT: AAA 90 ASN cc_start: 0.7380 (t0) cc_final: 0.7138 (t0) REVERT: AAA 120 VAL cc_start: 0.8310 (t) cc_final: 0.8043 (m) REVERT: AAA 151 THR cc_start: 0.8279 (m) cc_final: 0.8018 (p) REVERT: AAA 207 VAL cc_start: 0.8782 (t) cc_final: 0.8562 (m) REVERT: AAA 230 ILE cc_start: 0.7746 (mt) cc_final: 0.7501 (mm) REVERT: AAA 262 GLU cc_start: 0.6889 (pm20) cc_final: 0.6464 (pm20) REVERT: AAA 326 SER cc_start: 0.8029 (p) cc_final: 0.7706 (m) REVERT: AAA 373 VAL cc_start: 0.7525 (t) cc_final: 0.6879 (m) REVERT: AAA 460 LYS cc_start: 0.8364 (pttt) cc_final: 0.8006 (mtpp) REVERT: AAA 611 GLN cc_start: 0.7645 (mm110) cc_final: 0.7215 (mm-40) REVERT: AAA 712 ASN cc_start: 0.7613 (p0) cc_final: 0.7259 (p0) REVERT: AAA 715 ILE cc_start: 0.8289 (mm) cc_final: 0.8029 (mm) REVERT: AAA 872 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7738 (t) REVERT: AAA 920 TYR cc_start: 0.7255 (p90) cc_final: 0.6851 (p90) REVERT: AAA 936 TYR cc_start: 0.7829 (m-80) cc_final: 0.7549 (m-80) REVERT: AAA 991 THR cc_start: 0.7241 (m) cc_final: 0.6735 (p) REVERT: AAA 1015 GLN cc_start: 0.7348 (mp10) cc_final: 0.7014 (mp10) outliers start: 25 outliers final: 20 residues processed: 180 average time/residue: 0.0642 time to fit residues: 17.1438 Evaluate side-chains 186 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 270 TRP Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 527 LEU Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 818 TYR Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 1002 MET Chi-restraints excluded: chain AAA residue 1005 LEU Chi-restraints excluded: chain AAA residue 1034 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107882 restraints weight = 14162.497| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.34 r_work: 0.3213 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8923 Z= 0.157 Angle : 0.724 11.213 12398 Z= 0.329 Chirality : 0.045 0.262 1645 Planarity : 0.005 0.053 1433 Dihedral : 5.017 43.736 1152 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.79 % Allowed : 15.74 % Favored : 81.47 % 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: -0.28 (0.26), residues: 1038 helix: -0.58 (0.57), residues: 80 sheet: 0.68 (0.25), residues: 423 loop : -0.83 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 272 TYR 0.021 0.002 TYRAAA 672 PHE 0.021 0.002 PHEAAA 215 TRP 0.008 0.002 TRPAAA 270 HIS 0.002 0.001 HISAAA1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8859) covalent geometry : angle 0.68458 / 0.32 (12207) SS BOND : bond 0.00455 / 0.24 ( 1) SS BOND : angle 1.83563 / 1.00 ( 2) hydrogen bonds : bond 0.03335 / 2.26 ( 158) hydrogen bonds : angle 4.70234 / 3.13 ( 381) glycosidic custom : bond 0.00107 / 0.06 ( 11) glycosidic custom : angle 1.36480 / 0.91 ( 33) link_ALPHA1-4 : bond 0.00669 / 0.37 ( 7) link_ALPHA1-4 : angle 1.58035 / 0.97 ( 21) link_ALPHA1-6 : bond 0.00504 / 0.28 ( 9) link_ALPHA1-6 : angle 1.60795 / 0.94 ( 27) link_BETA1-4 : bond 0.00588 / 0.32 ( 17) link_BETA1-4 : angle 1.96827 / 1.22 ( 51) link_NAG-ASN : bond 0.00266 / 0.15 ( 19) link_NAG-ASN : angle 2.63663 / 1.62 ( 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 188 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 59 VAL cc_start: 0.8104 (t) cc_final: 0.7611 (m) REVERT: AAA 75 ILE cc_start: 0.7935 (pp) cc_final: 0.7683 (mt) REVERT: AAA 90 ASN cc_start: 0.7321 (t0) cc_final: 0.7081 (t0) REVERT: AAA 120 VAL cc_start: 0.8358 (t) cc_final: 0.8060 (m) REVERT: AAA 151 THR cc_start: 0.8253 (m) cc_final: 0.7974 (p) REVERT: AAA 207 VAL cc_start: 0.8782 (t) cc_final: 0.8571 (m) REVERT: AAA 230 ILE cc_start: 0.7769 (mt) cc_final: 0.7503 (mm) REVERT: AAA 262 GLU cc_start: 0.7078 (pm20) cc_final: 0.6614 (pm20) REVERT: AAA 326 SER cc_start: 0.8006 (p) cc_final: 0.7763 (m) REVERT: AAA 460 LYS cc_start: 0.8370 (pttt) cc_final: 0.8065 (mtpp) REVERT: AAA 573 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: AAA 575 MET cc_start: 0.7978 (mtt) cc_final: 0.7687 (mtm) REVERT: AAA 611 GLN cc_start: 0.7723 (mm110) cc_final: 0.7300 (mm-40) REVERT: AAA 635 THR cc_start: 0.8356 (t) cc_final: 0.7555 (p) REVERT: AAA 712 ASN cc_start: 0.7630 (p0) cc_final: 0.7269 (p0) REVERT: AAA 715 ILE cc_start: 0.8276 (mm) cc_final: 0.7980 (mt) REVERT: AAA 872 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7798 (t) REVERT: AAA 936 TYR cc_start: 0.7839 (m-80) cc_final: 0.7598 (m-80) REVERT: AAA 991 THR cc_start: 0.7222 (m) cc_final: 0.6682 (p) REVERT: AAA 1015 GLN cc_start: 0.7236 (mp10) cc_final: 0.6919 (mp10) outliers start: 25 outliers final: 22 residues processed: 177 average time/residue: 0.0621 time to fit residues: 16.2451 Evaluate side-chains 185 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 56 LEU Chi-restraints excluded: chain AAA residue 135 VAL Chi-restraints excluded: chain AAA residue 197 THR Chi-restraints excluded: chain AAA residue 208 VAL Chi-restraints excluded: chain AAA residue 227 VAL Chi-restraints excluded: chain AAA residue 298 VAL Chi-restraints excluded: chain AAA residue 404 THR Chi-restraints excluded: chain AAA residue 449 THR Chi-restraints excluded: chain AAA residue 457 ILE Chi-restraints excluded: chain AAA residue 527 LEU Chi-restraints excluded: chain AAA residue 573 GLU Chi-restraints excluded: chain AAA residue 578 MET Chi-restraints excluded: chain AAA residue 627 ASP Chi-restraints excluded: chain AAA residue 666 SER Chi-restraints excluded: chain AAA residue 677 CYS Chi-restraints excluded: chain AAA residue 799 VAL Chi-restraints excluded: chain AAA residue 817 MET Chi-restraints excluded: chain AAA residue 818 TYR Chi-restraints excluded: chain AAA residue 845 THR Chi-restraints excluded: chain AAA residue 872 VAL Chi-restraints excluded: chain AAA residue 877 SER Chi-restraints excluded: chain AAA residue 916 THR Chi-restraints excluded: chain AAA residue 1002 MET Chi-restraints excluded: chain AAA residue 1005 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.142243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108446 restraints weight = 14221.047| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.20 r_work: 0.3246 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8923 Z= 0.128 Angle : 0.684 10.112 12398 Z= 0.311 Chirality : 0.045 0.252 1645 Planarity : 0.005 0.052 1433 Dihedral : 4.889 43.647 1152 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.68 % Allowed : 15.96 % Favored : 81.36 % 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: -0.23 (0.26), residues: 1038 helix: -0.43 (0.59), residues: 80 sheet: 0.62 (0.25), residues: 434 loop : -0.74 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAAA 272 TYR 0.019 0.001 TYRAAA 672 PHE 0.010 0.001 PHEAAA 290 TRP 0.009 0.001 TRPAAA 960 HIS 0.002 0.001 HISAAA 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8859) covalent geometry : angle 0.64619 / 0.30 (12207) SS BOND : bond 0.00423 / 0.22 ( 1) SS BOND : angle 1.81015 / 0.99 ( 2) hydrogen bonds : bond 0.03056 / 2.06 ( 158) hydrogen bonds : angle 4.61477 / 3.07 ( 381) glycosidic custom : bond 0.00123 / 0.09 ( 11) glycosidic custom : angle 1.29161 / 0.86 ( 33) link_ALPHA1-4 : bond 0.00683 / 0.38 ( 7) link_ALPHA1-4 : angle 1.50989 / 0.93 ( 21) link_ALPHA1-6 : bond 0.00527 / 0.29 ( 9) link_ALPHA1-6 : angle 1.58876 / 0.94 ( 27) link_BETA1-4 : bond 0.00594 / 0.32 ( 17) link_BETA1-4 : angle 1.84111 / 1.13 ( 51) link_NAG-ASN : bond 0.00251 / 0.15 ( 19) link_NAG-ASN : angle 2.48970 / 1.56 ( 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: 1614.47 seconds wall clock time: 28 minutes 11.89 seconds (1691.89 seconds total)