Starting phenix.real_space_refine on Wed Sep 17 13:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ziv_60121/09_2025/8ziv_60121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ziv_60121/09_2025/8ziv_60121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ziv_60121/09_2025/8ziv_60121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ziv_60121/09_2025/8ziv_60121.map" model { file = "/net/cci-nas-00/data/ceres_data/8ziv_60121/09_2025/8ziv_60121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ziv_60121/09_2025/8ziv_60121.cif" } resolution = 2.95 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= 0.027 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 56 5.16 5 C 5518 2.51 5 N 1426 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8818 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1835 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "A" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4693 Classifications: {'peptide': 603} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 567} Chain: "C" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1755 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 220} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.54, per 1000 atoms: 0.29 Number of scatterers: 8818 At special positions: 0 Unit cell: (84.812, 112.772, 155.644, 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 56 16.00 O 1818 8.00 N 1426 7.00 C 5518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 826 " distance=2.03 Simple disulfide: pdb=" SG CYS D 896 " - pdb=" SG CYS A 772 " distance=2.03 Simple disulfide: pdb=" SG CYS D 910 " - pdb=" SG CYS D 977 " distance=2.03 Simple disulfide: pdb=" SG CYS D 941 " - pdb=" SG CYS D 956 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 422 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " BETA1-6 " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 801 " - " ASN A 706 " " NAG A 802 " - " ASN A 682 " " NAG A 803 " - " ASN A 328 " " NAG B 1 " - " ASN D 887 " " NAG D1101 " - " ASN D 848 " " NAG E 1 " - " ASN D 909 " " NAG F 1 " - " ASN D 949 " " NAG G 1 " - " ASN D 980 " " NAG H 1 " - " ASN A 534 " " NAG I 1 " - " ASN A 388 " " NAG J 1 " - " ASN A 440 " " NAG K 1 " - " ASN A 470 " " NAG L 1 " - " ASN A 503 " " NAG M 1 " - " ASN A 630 " " NAG N 1 " - " ASN A 725 " " NAG O 1 " - " ASN A 335 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 318.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 8.6% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 823 through 828 removed outlier: 3.634A pdb=" N VAL D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 835 No H-bonds generated for 'chain 'D' and resid 833 through 835' Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.973A pdb=" N GLN D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1019 removed outlier: 3.724A pdb=" N PHE D1017 " --> pdb=" O TRP D1013 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS D1019 " --> pdb=" O GLN D1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.885A pdb=" N GLU A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 4.113A pdb=" N SER A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.574A pdb=" N SER A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.636A pdb=" N TYR C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 Processing sheet with id=AA1, first strand: chain 'D' and resid 799 through 804 removed outlier: 3.682A pdb=" N CYS D 810 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR D 804 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 861 " --> pdb=" O HIS D 881 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 841 " --> pdb=" O VAL D 855 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 859 " --> pdb=" O TRP D 837 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TRP D 837 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 909 through 914 removed outlier: 3.682A pdb=" N GLY D 914 " --> pdb=" O GLN D 929 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS D 956 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL D1003 " --> pdb=" O SER D 990 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP D 983 " --> pdb=" O GLU D 979 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU D 979 " --> pdb=" O TRP D 983 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU D 985 " --> pdb=" O CYS D 977 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS D 977 " --> pdb=" O LEU D 985 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 913 " --> pdb=" O PRO D 974 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN D 978 " --> pdb=" O ASN D 909 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN D 909 " --> pdb=" O GLN D 978 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.527A pdb=" N ILE A 198 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.576A pdb=" N LEU A 316 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 279 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.723A pdb=" N THR A 312 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 306 removed outlier: 3.506A pdb=" N LYS A 266 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.233A pdb=" N LYS A 436 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.959A pdb=" N TYR A 393 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 12.643A pdb=" N PHE A 392 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 494 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 394 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU A 492 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS A 428 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP A 494 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP A 426 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 442 through 443 Processing sheet with id=AB1, first strand: chain 'A' and resid 529 through 530 removed outlier: 3.701A pdb=" N ASN A 557 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 594 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP A 584 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 592 " --> pdb=" O ASP A 584 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 565 Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 572 removed outlier: 3.678A pdb=" N GLU A 570 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 626 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AB5, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AB6, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 703 removed outlier: 3.747A pdb=" N LEU A 741 " --> pdb=" O CYS A 703 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 740 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 38 through 42 removed outlier: 4.049A pdb=" N CYS C 48 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 92 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 159 through 162 removed outlier: 6.932A pdb=" N VAL C 204 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 214 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N THR C 230 " --> pdb=" O VAL C 214 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 489 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: 1.60 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1461 1.29 - 1.42: 2254 1.42 - 1.55: 5232 1.55 - 1.68: 8 1.68 - 1.81: 68 Bond restraints: 9023 Sorted by residual: bond pdb=" N GLY A 683 " pdb=" CA GLY A 683 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.60e-03 1.09e+04 1.10e+01 bond pdb=" C7 NAG A 803 " pdb=" O7 NAG A 803 " ideal model delta sigma weight residual 1.222 1.156 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C2 NAG A 803 " pdb=" C3 NAG A 803 " ideal model delta sigma weight residual 1.526 1.466 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" C4 NAG A 802 " pdb=" O4 NAG A 802 " ideal model delta sigma weight residual 1.409 1.468 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.42e+00 ... (remaining 9018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12027 2.45 - 4.90: 199 4.90 - 7.34: 51 7.34 - 9.79: 6 9.79 - 12.24: 2 Bond angle restraints: 12285 Sorted by residual: angle pdb=" CA ASN A 682 " pdb=" CB ASN A 682 " pdb=" CG ASN A 682 " ideal model delta sigma weight residual 112.60 121.75 -9.15 1.00e+00 1.00e+00 8.37e+01 angle pdb=" C ASN A 328 " pdb=" N ALA A 329 " pdb=" CA ALA A 329 " ideal model delta sigma weight residual 122.33 111.24 11.09 1.68e+00 3.54e-01 4.36e+01 angle pdb=" C ASN A 682 " pdb=" N GLY A 683 " pdb=" CA GLY A 683 " ideal model delta sigma weight residual 122.30 116.77 5.53 1.03e+00 9.43e-01 2.88e+01 angle pdb=" C ASN A 328 " pdb=" CA ASN A 328 " pdb=" CB ASN A 328 " ideal model delta sigma weight residual 109.35 118.13 -8.78 1.98e+00 2.55e-01 1.96e+01 angle pdb=" C PHE A 327 " pdb=" N ASN A 328 " pdb=" CA ASN A 328 " ideal model delta sigma weight residual 122.73 129.81 -7.08 1.62e+00 3.81e-01 1.91e+01 ... (remaining 12280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 5624 23.70 - 47.41: 108 47.41 - 71.11: 35 71.11 - 94.81: 71 94.81 - 118.52: 45 Dihedral angle restraints: 5883 sinusoidal: 2826 harmonic: 3057 Sorted by residual: dihedral pdb=" C ASN A 328 " pdb=" N ASN A 328 " pdb=" CA ASN A 328 " pdb=" CB ASN A 328 " ideal model delta harmonic sigma weight residual -122.60 -137.14 14.54 0 2.50e+00 1.60e-01 3.38e+01 dihedral pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CA ASN A 328 " pdb=" CB ASN A 328 " ideal model delta harmonic sigma weight residual 122.80 134.28 -11.48 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" C2 MAN J 4 " pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " pdb=" C5 MAN J 4 " ideal model delta sinusoidal sigma weight residual -57.62 60.90 -118.52 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 5880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 1432 0.153 - 0.306: 22 0.306 - 0.460: 1 0.460 - 0.613: 2 0.613 - 0.766: 1 Chirality restraints: 1458 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 470 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.96 -0.57 2.00e-01 2.50e+01 8.06e+00 ... (remaining 1455 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.317 2.00e-02 2.50e+03 2.69e-01 9.07e+02 pdb=" C7 NAG G 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.468 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 803 " 0.195 2.00e-02 2.50e+03 1.62e-01 3.26e+02 pdb=" C7 NAG A 803 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG A 803 " 0.138 2.00e-02 2.50e+03 pdb=" N2 NAG A 803 " -0.265 2.00e-02 2.50e+03 pdb=" O7 NAG A 803 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " -0.107 2.00e-02 2.50e+03 9.02e-02 1.02e+02 pdb=" C7 NAG A 802 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.010 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 4 1.84 - 2.61: 129 2.61 - 3.37: 10790 3.37 - 4.14: 20930 4.14 - 4.90: 36299 Nonbonded interactions: 68152 Sorted by model distance: nonbonded pdb=" OE1 GLU A 432 " pdb=" CB SER C 195 " model vdw 1.078 3.440 nonbonded pdb=" OE2 GLU A 432 " pdb=" O SER C 195 " model vdw 1.146 3.040 nonbonded pdb=" CD1 LEU A 622 " pdb=" CD2 LEU C 189 " model vdw 1.660 3.880 nonbonded pdb=" OE2 GLU A 432 " pdb=" C SER C 195 " model vdw 1.679 3.270 nonbonded pdb=" OE1 GLU A 432 " pdb=" OG SER C 195 " model vdw 1.865 3.040 ... (remaining 68147 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 'B' selection = chain 'E' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 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 : 0.004 0.066 9079 Z= 0.231 Angle : 0.853 20.593 12438 Z= 0.372 Chirality : 0.061 0.766 1458 Planarity : 0.009 0.269 1560 Dihedral : 18.272 118.518 3886 Min Nonbonded Distance : 1.078 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.92 % Favored : 93.52 % Rotamer: Outliers : 1.85 % Allowed : 3.05 % Favored : 95.09 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.27), residues: 1064 helix: 1.77 (0.77), residues: 56 sheet: 0.91 (0.33), residues: 270 loop : -0.50 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 368 TYR 0.005 0.001 TYR A 546 PHE 0.007 0.001 PHE A 334 TRP 0.003 0.000 TRP A 366 HIS 0.001 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9023) covalent geometry : angle 0.74430 (12285) SS BOND : bond 0.00121 ( 15) SS BOND : angle 0.46905 ( 30) hydrogen bonds : bond 0.25283 ( 186) hydrogen bonds : angle 10.10215 ( 489) link_ALPHA1-3 : bond 0.00777 ( 1) link_ALPHA1-3 : angle 1.47110 ( 3) link_ALPHA1-6 : bond 0.00342 ( 2) link_ALPHA1-6 : angle 1.67782 ( 6) link_BETA1-4 : bond 0.00937 ( 21) link_BETA1-4 : angle 3.63939 ( 63) link_BETA1-6 : bond 0.00683 ( 1) link_BETA1-6 : angle 1.27728 ( 3) link_NAG-ASN : bond 0.01169 ( 16) link_NAG-ASN : angle 5.34567 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.3911 (OUTLIER) cc_final: 0.3409 (m-80) REVERT: A 295 SER cc_start: 0.6108 (t) cc_final: 0.5895 (p) REVERT: A 548 ASN cc_start: 0.5746 (m-40) cc_final: 0.4874 (m-40) REVERT: A 619 ASN cc_start: 0.4426 (OUTLIER) cc_final: 0.3336 (p0) REVERT: A 622 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4497 (tp) REVERT: C 57 TRP cc_start: 0.6108 (m100) cc_final: 0.5000 (m100) REVERT: C 98 GLN cc_start: 0.7126 (mt0) cc_final: 0.6874 (mt0) outliers start: 17 outliers final: 10 residues processed: 134 average time/residue: 0.3808 time to fit residues: 56.3496 Evaluate side-chains 122 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 871 ARG Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 844 HIS D 881 HIS D 921 GLN D 929 GLN A 310 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 619 ASN A 647 HIS A 700 HIS A 768 ASN C 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.255937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.229060 restraints weight = 14021.241| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 3.07 r_work: 0.4591 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9079 Z= 0.215 Angle : 0.870 13.324 12438 Z= 0.388 Chirality : 0.055 0.572 1458 Planarity : 0.005 0.046 1560 Dihedral : 16.960 89.319 2004 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.89 % Favored : 91.73 % Rotamer: Outliers : 3.16 % Allowed : 8.07 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1064 helix: 1.20 (0.73), residues: 60 sheet: 0.49 (0.32), residues: 265 loop : -0.76 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.016 0.002 TYR D 868 PHE 0.029 0.002 PHE A 568 TRP 0.022 0.002 TRP D 819 HIS 0.012 0.002 HIS D 881 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9023) covalent geometry : angle 0.79117 (12285) SS BOND : bond 0.00322 ( 15) SS BOND : angle 0.98704 ( 30) hydrogen bonds : bond 0.04961 ( 186) hydrogen bonds : angle 7.04515 ( 489) link_ALPHA1-3 : bond 0.01032 ( 1) link_ALPHA1-3 : angle 2.25298 ( 3) link_ALPHA1-6 : bond 0.00325 ( 2) link_ALPHA1-6 : angle 2.06824 ( 6) link_BETA1-4 : bond 0.00904 ( 21) link_BETA1-4 : angle 3.80736 ( 63) link_BETA1-6 : bond 0.00891 ( 1) link_BETA1-6 : angle 2.28211 ( 3) link_NAG-ASN : bond 0.00735 ( 16) link_NAG-ASN : angle 3.86788 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6595 (Cg_endo) cc_final: 0.6373 (Cg_exo) REVERT: A 272 PHE cc_start: 0.3954 (OUTLIER) cc_final: 0.3622 (m-80) REVERT: A 277 THR cc_start: 0.7569 (p) cc_final: 0.7186 (t) REVERT: A 328 ASN cc_start: 0.3357 (OUTLIER) cc_final: 0.2733 (m110) REVERT: A 569 GLN cc_start: 0.6386 (tp40) cc_final: 0.6182 (tp40) REVERT: A 619 ASN cc_start: 0.4378 (OUTLIER) cc_final: 0.4110 (p0) REVERT: A 682 ASN cc_start: 0.2269 (OUTLIER) cc_final: 0.1731 (p0) outliers start: 29 outliers final: 8 residues processed: 124 average time/residue: 0.3970 time to fit residues: 54.1109 Evaluate side-chains 112 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain C residue 23 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN C 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.256812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.230070 restraints weight = 14107.021| |-----------------------------------------------------------------------------| r_work (start): 0.4701 rms_B_bonded: 3.03 r_work: 0.4602 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9079 Z= 0.149 Angle : 0.767 13.615 12438 Z= 0.334 Chirality : 0.052 0.560 1458 Planarity : 0.004 0.050 1560 Dihedral : 14.117 80.509 1994 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.86 % Favored : 92.76 % Rotamer: Outliers : 2.73 % Allowed : 9.60 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.26), residues: 1064 helix: 1.33 (0.74), residues: 60 sheet: 0.29 (0.31), residues: 281 loop : -0.77 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 611 TYR 0.009 0.001 TYR D 803 PHE 0.019 0.002 PHE A 374 TRP 0.029 0.002 TRP D 819 HIS 0.004 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9023) covalent geometry : angle 0.68896 (12285) SS BOND : bond 0.00319 ( 15) SS BOND : angle 0.76865 ( 30) hydrogen bonds : bond 0.04088 ( 186) hydrogen bonds : angle 6.66564 ( 489) link_ALPHA1-3 : bond 0.02038 ( 1) link_ALPHA1-3 : angle 2.41110 ( 3) link_ALPHA1-6 : bond 0.00243 ( 2) link_ALPHA1-6 : angle 1.86247 ( 6) link_BETA1-4 : bond 0.01009 ( 21) link_BETA1-4 : angle 3.54894 ( 63) link_BETA1-6 : bond 0.01022 ( 1) link_BETA1-6 : angle 1.96606 ( 3) link_NAG-ASN : bond 0.00582 ( 16) link_NAG-ASN : angle 3.58562 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6531 (Cg_endo) cc_final: 0.6318 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6217 (m-80) cc_final: 0.5966 (m-80) REVERT: A 272 PHE cc_start: 0.4208 (OUTLIER) cc_final: 0.3665 (m-80) REVERT: A 277 THR cc_start: 0.7541 (p) cc_final: 0.7181 (t) REVERT: A 328 ASN cc_start: 0.3488 (OUTLIER) cc_final: 0.2658 (m-40) REVERT: A 548 ASN cc_start: 0.6133 (m-40) cc_final: 0.5335 (m110) outliers start: 25 outliers final: 14 residues processed: 119 average time/residue: 0.3831 time to fit residues: 50.2509 Evaluate side-chains 115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 885 LYS Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain C residue 23 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.256075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.229139 restraints weight = 14161.974| |-----------------------------------------------------------------------------| r_work (start): 0.4697 rms_B_bonded: 3.06 r_work: 0.4593 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9079 Z= 0.138 Angle : 0.733 13.392 12438 Z= 0.322 Chirality : 0.051 0.566 1458 Planarity : 0.004 0.052 1560 Dihedral : 11.478 70.917 1989 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.05 % Favored : 92.58 % Rotamer: Outliers : 3.71 % Allowed : 9.81 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.26), residues: 1064 helix: 1.16 (0.73), residues: 60 sheet: 0.18 (0.31), residues: 281 loop : -0.83 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 611 TYR 0.014 0.001 TYR D1004 PHE 0.047 0.002 PHE A 374 TRP 0.033 0.002 TRP D 819 HIS 0.004 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9023) covalent geometry : angle 0.65978 (12285) SS BOND : bond 0.00242 ( 15) SS BOND : angle 0.67434 ( 30) hydrogen bonds : bond 0.03430 ( 186) hydrogen bonds : angle 6.32953 ( 489) link_ALPHA1-3 : bond 0.02402 ( 1) link_ALPHA1-3 : angle 2.56569 ( 3) link_ALPHA1-6 : bond 0.00288 ( 2) link_ALPHA1-6 : angle 1.85536 ( 6) link_BETA1-4 : bond 0.01012 ( 21) link_BETA1-4 : angle 3.44135 ( 63) link_BETA1-6 : bond 0.01053 ( 1) link_BETA1-6 : angle 1.99069 ( 3) link_NAG-ASN : bond 0.00572 ( 16) link_NAG-ASN : angle 3.30664 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6577 (Cg_endo) cc_final: 0.6355 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5106 (pt) REVERT: D 976 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5044 (mtt) REVERT: D 1017 PHE cc_start: 0.6365 (m-80) cc_final: 0.6105 (m-80) REVERT: A 272 PHE cc_start: 0.4243 (OUTLIER) cc_final: 0.3682 (m-80) REVERT: A 277 THR cc_start: 0.7531 (p) cc_final: 0.7170 (t) REVERT: A 316 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6671 (tm) REVERT: A 328 ASN cc_start: 0.3313 (OUTLIER) cc_final: 0.2855 (m-40) REVERT: A 357 VAL cc_start: 0.6101 (OUTLIER) cc_final: 0.5495 (m) REVERT: A 528 PHE cc_start: 0.5031 (OUTLIER) cc_final: 0.4708 (m-10) REVERT: A 565 GLN cc_start: 0.7590 (tt0) cc_final: 0.7358 (tt0) outliers start: 34 outliers final: 16 residues processed: 120 average time/residue: 0.3809 time to fit residues: 50.5883 Evaluate side-chains 120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 98 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1015 GLN A 209 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 466 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.254465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.227375 restraints weight = 13934.509| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 3.02 r_work: 0.4574 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9079 Z= 0.171 Angle : 0.749 13.556 12438 Z= 0.337 Chirality : 0.051 0.568 1458 Planarity : 0.004 0.051 1560 Dihedral : 10.852 71.457 1989 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.05 % Favored : 92.58 % Rotamer: Outliers : 4.25 % Allowed : 9.81 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.26), residues: 1064 helix: 1.44 (0.77), residues: 54 sheet: 0.06 (0.31), residues: 275 loop : -0.98 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.015 0.002 TYR D 868 PHE 0.035 0.002 PHE A 374 TRP 0.029 0.002 TRP D 819 HIS 0.006 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9023) covalent geometry : angle 0.67673 (12285) SS BOND : bond 0.00313 ( 15) SS BOND : angle 1.20496 ( 30) hydrogen bonds : bond 0.03670 ( 186) hydrogen bonds : angle 6.59366 ( 489) link_ALPHA1-3 : bond 0.02190 ( 1) link_ALPHA1-3 : angle 2.34172 ( 3) link_ALPHA1-6 : bond 0.00231 ( 2) link_ALPHA1-6 : angle 1.73407 ( 6) link_BETA1-4 : bond 0.01005 ( 21) link_BETA1-4 : angle 3.36434 ( 63) link_BETA1-6 : bond 0.00929 ( 1) link_BETA1-6 : angle 1.91527 ( 3) link_NAG-ASN : bond 0.00619 ( 16) link_NAG-ASN : angle 3.40588 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6675 (Cg_endo) cc_final: 0.6448 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5142 (pt) REVERT: D 976 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5431 (mtt) REVERT: D 1017 PHE cc_start: 0.6516 (m-80) cc_final: 0.6233 (m-80) REVERT: A 272 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3804 (m-80) REVERT: A 316 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6631 (tm) REVERT: A 328 ASN cc_start: 0.3473 (OUTLIER) cc_final: 0.2952 (m110) REVERT: A 578 ASP cc_start: 0.6859 (m-30) cc_final: 0.6639 (m-30) REVERT: A 622 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5308 (tt) outliers start: 39 outliers final: 18 residues processed: 120 average time/residue: 0.3965 time to fit residues: 52.3381 Evaluate side-chains 120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 98 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 34 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 953 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.254769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.228085 restraints weight = 13944.389| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 2.98 r_work: 0.4577 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9079 Z= 0.137 Angle : 0.729 13.395 12438 Z= 0.325 Chirality : 0.051 0.566 1458 Planarity : 0.004 0.048 1560 Dihedral : 10.363 70.973 1989 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.14 % Favored : 92.48 % Rotamer: Outliers : 3.71 % Allowed : 10.69 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.26), residues: 1064 helix: 1.43 (0.77), residues: 54 sheet: -0.01 (0.31), residues: 275 loop : -0.99 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.009 0.001 TYR D 868 PHE 0.032 0.002 PHE A 374 TRP 0.034 0.002 TRP D 819 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9023) covalent geometry : angle 0.65339 (12285) SS BOND : bond 0.00308 ( 15) SS BOND : angle 1.21187 ( 30) hydrogen bonds : bond 0.03256 ( 186) hydrogen bonds : angle 6.42877 ( 489) link_ALPHA1-3 : bond 0.02314 ( 1) link_ALPHA1-3 : angle 2.34334 ( 3) link_ALPHA1-6 : bond 0.00301 ( 2) link_ALPHA1-6 : angle 1.60721 ( 6) link_BETA1-4 : bond 0.00998 ( 21) link_BETA1-4 : angle 3.29946 ( 63) link_BETA1-6 : bond 0.01024 ( 1) link_BETA1-6 : angle 1.96102 ( 3) link_NAG-ASN : bond 0.00594 ( 16) link_NAG-ASN : angle 3.53543 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6618 (Cg_endo) cc_final: 0.6403 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6344 (OUTLIER) cc_final: 0.5230 (pt) REVERT: D 1017 PHE cc_start: 0.6460 (m-80) cc_final: 0.6228 (m-80) REVERT: A 272 PHE cc_start: 0.4271 (OUTLIER) cc_final: 0.3712 (m-80) REVERT: A 277 THR cc_start: 0.7448 (p) cc_final: 0.7074 (t) REVERT: A 316 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6729 (tm) REVERT: A 328 ASN cc_start: 0.3412 (OUTLIER) cc_final: 0.2999 (m-40) REVERT: A 578 ASP cc_start: 0.6870 (m-30) cc_final: 0.6661 (m-30) REVERT: A 622 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5359 (tt) outliers start: 34 outliers final: 21 residues processed: 122 average time/residue: 0.3708 time to fit residues: 50.1312 Evaluate side-chains 127 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 893 GLN Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 98 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 953 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN A 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.253486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.226916 restraints weight = 13943.596| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 2.97 r_work: 0.4568 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9079 Z= 0.147 Angle : 0.728 13.190 12438 Z= 0.325 Chirality : 0.050 0.562 1458 Planarity : 0.004 0.059 1560 Dihedral : 10.137 70.940 1989 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.14 % Favored : 92.48 % Rotamer: Outliers : 4.36 % Allowed : 10.36 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.26), residues: 1064 helix: 1.47 (0.77), residues: 54 sheet: -0.08 (0.31), residues: 280 loop : -1.06 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.011 0.001 TYR D 868 PHE 0.032 0.002 PHE A 374 TRP 0.032 0.002 TRP D 819 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9023) covalent geometry : angle 0.65453 (12285) SS BOND : bond 0.00434 ( 15) SS BOND : angle 1.17673 ( 30) hydrogen bonds : bond 0.03341 ( 186) hydrogen bonds : angle 6.33060 ( 489) link_ALPHA1-3 : bond 0.02156 ( 1) link_ALPHA1-3 : angle 2.29155 ( 3) link_ALPHA1-6 : bond 0.00315 ( 2) link_ALPHA1-6 : angle 1.59639 ( 6) link_BETA1-4 : bond 0.00991 ( 21) link_BETA1-4 : angle 3.27956 ( 63) link_BETA1-6 : bond 0.00972 ( 1) link_BETA1-6 : angle 1.93489 ( 3) link_NAG-ASN : bond 0.00568 ( 16) link_NAG-ASN : angle 3.45034 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6638 (Cg_endo) cc_final: 0.6426 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5169 (pt) REVERT: D 1017 PHE cc_start: 0.6549 (m-80) cc_final: 0.6271 (m-80) REVERT: A 272 PHE cc_start: 0.4280 (OUTLIER) cc_final: 0.3755 (m-80) REVERT: A 277 THR cc_start: 0.7484 (p) cc_final: 0.7104 (t) REVERT: A 316 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6667 (tm) REVERT: A 328 ASN cc_start: 0.3376 (OUTLIER) cc_final: 0.2954 (m-40) REVERT: A 578 ASP cc_start: 0.6874 (m-30) cc_final: 0.6656 (m-30) REVERT: A 622 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5188 (tt) outliers start: 40 outliers final: 23 residues processed: 124 average time/residue: 0.3564 time to fit residues: 49.1051 Evaluate side-chains 127 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 VAL Chi-restraints excluded: chain D residue 893 GLN Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 53 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 37 optimal weight: 0.0030 overall best weight: 1.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 953 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 453 GLN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.250643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.223942 restraints weight = 13635.595| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 2.95 r_work: 0.4540 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9079 Z= 0.201 Angle : 0.775 13.085 12438 Z= 0.354 Chirality : 0.052 0.560 1458 Planarity : 0.005 0.068 1560 Dihedral : 10.158 69.585 1989 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.46 % Favored : 91.17 % Rotamer: Outliers : 4.14 % Allowed : 11.23 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.26), residues: 1064 helix: 1.36 (0.79), residues: 54 sheet: -0.30 (0.32), residues: 272 loop : -1.23 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 611 TYR 0.034 0.002 TYR A 427 PHE 0.034 0.002 PHE A 374 TRP 0.040 0.002 TRP D 819 HIS 0.006 0.002 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9023) covalent geometry : angle 0.70474 (12285) SS BOND : bond 0.00393 ( 15) SS BOND : angle 1.23984 ( 30) hydrogen bonds : bond 0.03794 ( 186) hydrogen bonds : angle 6.43525 ( 489) link_ALPHA1-3 : bond 0.02056 ( 1) link_ALPHA1-3 : angle 2.17528 ( 3) link_ALPHA1-6 : bond 0.00241 ( 2) link_ALPHA1-6 : angle 1.65012 ( 6) link_BETA1-4 : bond 0.00983 ( 21) link_BETA1-4 : angle 3.30352 ( 63) link_BETA1-6 : bond 0.00857 ( 1) link_BETA1-6 : angle 1.88521 ( 3) link_NAG-ASN : bond 0.00634 ( 16) link_NAG-ASN : angle 3.51378 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.313 Fit side-chains REVERT: D 906 PRO cc_start: 0.6712 (Cg_endo) cc_final: 0.6496 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6339 (OUTLIER) cc_final: 0.5225 (pt) REVERT: D 1017 PHE cc_start: 0.6643 (m-80) cc_final: 0.6356 (m-80) REVERT: A 272 PHE cc_start: 0.4302 (OUTLIER) cc_final: 0.3782 (m-80) REVERT: A 316 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6693 (tm) REVERT: A 328 ASN cc_start: 0.3352 (OUTLIER) cc_final: 0.3018 (m-40) REVERT: A 578 ASP cc_start: 0.6840 (m-30) cc_final: 0.6572 (m-30) REVERT: A 619 ASN cc_start: 0.5531 (OUTLIER) cc_final: 0.5191 (p0) outliers start: 38 outliers final: 23 residues processed: 121 average time/residue: 0.3589 time to fit residues: 47.8674 Evaluate side-chains 122 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 VAL Chi-restraints excluded: chain D residue 893 GLN Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 98 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.250653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.224370 restraints weight = 13611.565| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 2.93 r_work: 0.4548 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9079 Z= 0.171 Angle : 0.763 13.040 12438 Z= 0.346 Chirality : 0.051 0.557 1458 Planarity : 0.004 0.065 1560 Dihedral : 10.016 71.254 1989 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.08 % Favored : 91.54 % Rotamer: Outliers : 3.38 % Allowed : 12.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.26), residues: 1064 helix: 1.16 (0.77), residues: 55 sheet: -0.31 (0.32), residues: 270 loop : -1.25 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 611 TYR 0.040 0.002 TYR A 427 PHE 0.033 0.002 PHE A 374 TRP 0.046 0.002 TRP D 819 HIS 0.005 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9023) covalent geometry : angle 0.69309 (12285) SS BOND : bond 0.00361 ( 15) SS BOND : angle 1.21079 ( 30) hydrogen bonds : bond 0.03583 ( 186) hydrogen bonds : angle 6.47148 ( 489) link_ALPHA1-3 : bond 0.02084 ( 1) link_ALPHA1-3 : angle 2.14018 ( 3) link_ALPHA1-6 : bond 0.00268 ( 2) link_ALPHA1-6 : angle 1.59350 ( 6) link_BETA1-4 : bond 0.00972 ( 21) link_BETA1-4 : angle 3.26639 ( 63) link_BETA1-6 : bond 0.00928 ( 1) link_BETA1-6 : angle 1.90482 ( 3) link_NAG-ASN : bond 0.00600 ( 16) link_NAG-ASN : angle 3.45959 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.310 Fit side-chains REVERT: D 836 LYS cc_start: 0.7855 (tptt) cc_final: 0.7636 (tptt) REVERT: D 906 PRO cc_start: 0.6697 (Cg_endo) cc_final: 0.6482 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5242 (pt) REVERT: D 1017 PHE cc_start: 0.6705 (m-80) cc_final: 0.6407 (m-80) REVERT: A 272 PHE cc_start: 0.4271 (OUTLIER) cc_final: 0.3770 (m-80) REVERT: A 316 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6683 (tm) REVERT: A 328 ASN cc_start: 0.3321 (OUTLIER) cc_final: 0.2999 (m-40) REVERT: A 578 ASP cc_start: 0.6849 (m-30) cc_final: 0.6602 (m-30) outliers start: 31 outliers final: 21 residues processed: 116 average time/residue: 0.3936 time to fit residues: 50.3039 Evaluate side-chains 121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 893 GLN Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 98 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN A 619 ASN A 769 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.247254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.220473 restraints weight = 13358.463| |-----------------------------------------------------------------------------| r_work (start): 0.4613 rms_B_bonded: 2.90 r_work: 0.4510 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9079 Z= 0.274 Angle : 0.871 12.882 12438 Z= 0.407 Chirality : 0.056 0.561 1458 Planarity : 0.005 0.082 1560 Dihedral : 10.519 70.898 1989 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.77 % Favored : 89.85 % Rotamer: Outliers : 3.38 % Allowed : 12.43 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.25), residues: 1064 helix: 0.36 (0.72), residues: 61 sheet: -0.53 (0.32), residues: 258 loop : -1.54 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 611 TYR 0.038 0.003 TYR A 427 PHE 0.037 0.003 PHE A 374 TRP 0.066 0.004 TRP D 819 HIS 0.010 0.003 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9023) covalent geometry : angle 0.80510 (12285) SS BOND : bond 0.00534 ( 15) SS BOND : angle 1.32878 ( 30) hydrogen bonds : bond 0.04553 ( 186) hydrogen bonds : angle 6.98875 ( 489) link_ALPHA1-3 : bond 0.02120 ( 1) link_ALPHA1-3 : angle 1.91216 ( 3) link_ALPHA1-6 : bond 0.00103 ( 2) link_ALPHA1-6 : angle 1.81228 ( 6) link_BETA1-4 : bond 0.00960 ( 21) link_BETA1-4 : angle 3.33350 ( 63) link_BETA1-6 : bond 0.00761 ( 1) link_BETA1-6 : angle 1.87600 ( 3) link_NAG-ASN : bond 0.00697 ( 16) link_NAG-ASN : angle 3.75057 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.239 Fit side-chains REVERT: D 906 PRO cc_start: 0.6884 (Cg_endo) cc_final: 0.6650 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5216 (pt) REVERT: D 1017 PHE cc_start: 0.6776 (m-80) cc_final: 0.6465 (m-80) REVERT: A 272 PHE cc_start: 0.4370 (OUTLIER) cc_final: 0.3878 (m-80) REVERT: A 316 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6759 (tm) REVERT: A 324 TYR cc_start: 0.6414 (t80) cc_final: 0.6155 (t80) REVERT: A 328 ASN cc_start: 0.3499 (OUTLIER) cc_final: 0.3177 (m-40) REVERT: A 350 GLU cc_start: 0.7299 (pm20) cc_final: 0.6924 (pm20) REVERT: A 357 VAL cc_start: 0.6365 (OUTLIER) cc_final: 0.5900 (m) REVERT: A 578 ASP cc_start: 0.6884 (m-30) cc_final: 0.6582 (m-30) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 0.3811 time to fit residues: 53.9198 Evaluate side-chains 130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 885 LYS Chi-restraints excluded: chain D residue 893 GLN Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 183 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.0020 chunk 29 optimal weight: 0.0370 chunk 85 optimal weight: 0.0970 chunk 8 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 overall best weight: 0.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 865 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN A 463 ASN A 769 HIS C 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.251001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.224971 restraints weight = 13694.369| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 2.99 r_work: 0.4557 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9079 Z= 0.128 Angle : 0.758 12.967 12438 Z= 0.343 Chirality : 0.050 0.550 1458 Planarity : 0.005 0.065 1560 Dihedral : 9.701 70.548 1989 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.67 % Favored : 92.95 % Rotamer: Outliers : 2.29 % Allowed : 14.50 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.26), residues: 1064 helix: 1.09 (0.76), residues: 55 sheet: -0.51 (0.32), residues: 261 loop : -1.33 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 908 TYR 0.025 0.002 TYR A 427 PHE 0.027 0.002 PHE A 374 TRP 0.048 0.002 TRP D 819 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9023) covalent geometry : angle 0.68369 (12285) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.91034 ( 30) hydrogen bonds : bond 0.03209 ( 186) hydrogen bonds : angle 6.59125 ( 489) link_ALPHA1-3 : bond 0.02168 ( 1) link_ALPHA1-3 : angle 2.11968 ( 3) link_ALPHA1-6 : bond 0.00418 ( 2) link_ALPHA1-6 : angle 1.46855 ( 6) link_BETA1-4 : bond 0.01065 ( 21) link_BETA1-4 : angle 3.23167 ( 63) link_BETA1-6 : bond 0.01100 ( 1) link_BETA1-6 : angle 1.94369 ( 3) link_NAG-ASN : bond 0.00601 ( 16) link_NAG-ASN : angle 3.76295 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.97 seconds wall clock time: 52 minutes 25.38 seconds (3145.38 seconds total)