Starting phenix.real_space_refine on Sat Jun 7 14:32:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ziv_60121/06_2025/8ziv_60121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ziv_60121/06_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_60121/06_2025/8ziv_60121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ziv_60121/06_2025/8ziv_60121.map" model { file = "/net/cci-nas-00/data/ceres_data/8ziv_60121/06_2025/8ziv_60121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ziv_60121/06_2025/8ziv_60121.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.40, per 1000 atoms: 0.61 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: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 3.03 Time building geometry restraints manager: 3.12 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: 1.120 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.270 ------------------------------------------------------------------------------- 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 : 11.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.000 TRP A 366 HIS 0.001 0.000 HIS C 63 PHE 0.007 0.001 PHE A 334 TYR 0.005 0.001 TYR A 546 ARG 0.001 0.000 ARG A 368 Details of bonding type rmsd link_NAG-ASN : bond 0.01169 ( 16) link_NAG-ASN : angle 5.34567 ( 48) 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_ALPHA1-3 : bond 0.00777 ( 1) link_ALPHA1-3 : angle 1.47110 ( 3) hydrogen bonds : bond 0.25283 ( 186) hydrogen bonds : angle 10.10215 ( 489) link_BETA1-6 : bond 0.00683 ( 1) link_BETA1-6 : angle 1.27728 ( 3) SS BOND : bond 0.00121 ( 15) SS BOND : angle 0.46905 ( 30) covalent geometry : bond 0.00428 ( 9023) covalent geometry : angle 0.74430 (12285) *********************** 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 : 0.908 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: 0.7706 time to fit residues: 114.2178 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 : 0.880 ------------------------------------------------------------------------------- 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 89 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 361 ASN A 435 HIS A 619 ASN 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 = 0.4951 r_free = 0.4951 target = 0.258541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.232374 restraints weight = 14240.423| |-----------------------------------------------------------------------------| r_work (start): 0.4712 rms_B_bonded: 3.03 r_work: 0.4617 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.1665 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= 0.177 Angle : 0.807 13.376 12438 Z= 0.357 Chirality : 0.053 0.564 1458 Planarity : 0.004 0.042 1560 Dihedral : 17.492 91.746 2004 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.52 % Favored : 92.11 % Rotamer: Outliers : 2.73 % Allowed : 8.18 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1064 helix: 1.40 (0.74), residues: 60 sheet: 0.62 (0.32), residues: 269 loop : -0.66 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 819 HIS 0.011 0.002 HIS D 881 PHE 0.024 0.002 PHE A 568 TYR 0.012 0.002 TYR C 45 ARG 0.006 0.001 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 16) link_NAG-ASN : angle 3.77901 ( 48) link_ALPHA1-6 : bond 0.00237 ( 2) link_ALPHA1-6 : angle 2.02393 ( 6) link_BETA1-4 : bond 0.00982 ( 21) link_BETA1-4 : angle 3.67136 ( 63) link_ALPHA1-3 : bond 0.01604 ( 1) link_ALPHA1-3 : angle 2.41216 ( 3) hydrogen bonds : bond 0.04921 ( 186) hydrogen bonds : angle 7.16039 ( 489) link_BETA1-6 : bond 0.01142 ( 1) link_BETA1-6 : angle 2.12873 ( 3) SS BOND : bond 0.00252 ( 15) SS BOND : angle 0.97609 ( 30) covalent geometry : bond 0.00363 ( 9023) covalent geometry : angle 0.72654 (12285) *********************** 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 130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 272 PHE cc_start: 0.3861 (OUTLIER) cc_final: 0.3538 (m-80) REVERT: A 277 THR cc_start: 0.7460 (p) cc_final: 0.7081 (t) REVERT: A 324 TYR cc_start: 0.5091 (t80) cc_final: 0.4886 (t80) REVERT: A 328 ASN cc_start: 0.3366 (OUTLIER) cc_final: 0.2789 (m-40) REVERT: A 548 ASN cc_start: 0.6088 (m-40) cc_final: 0.5017 (m110) REVERT: A 569 GLN cc_start: 0.6194 (tp40) cc_final: 0.5894 (tp40) REVERT: A 619 ASN cc_start: 0.4291 (OUTLIER) cc_final: 0.3959 (p0) REVERT: A 682 ASN cc_start: 0.2288 (OUTLIER) cc_final: 0.1905 (p0) REVERT: C 98 GLN cc_start: 0.7169 (mt0) cc_final: 0.6952 (mt0) outliers start: 25 outliers final: 8 residues processed: 122 average time/residue: 0.8520 time to fit residues: 114.2881 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 : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 863 VAL 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 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 72 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.257582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.230979 restraints weight = 14192.846| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 3.05 r_work: 0.4605 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9079 Z= 0.144 Angle : 0.755 13.450 12438 Z= 0.329 Chirality : 0.052 0.555 1458 Planarity : 0.004 0.043 1560 Dihedral : 13.693 77.899 1994 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.39 % Favored : 93.23 % Rotamer: Outliers : 3.27 % Allowed : 8.83 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1064 helix: 1.35 (0.74), residues: 60 sheet: 0.34 (0.31), residues: 281 loop : -0.69 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 819 HIS 0.006 0.001 HIS D 844 PHE 0.024 0.002 PHE A 568 TYR 0.012 0.001 TYR D 948 ARG 0.006 0.001 ARG D 871 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 16) link_NAG-ASN : angle 3.53990 ( 48) link_ALPHA1-6 : bond 0.00252 ( 2) link_ALPHA1-6 : angle 1.83852 ( 6) link_BETA1-4 : bond 0.01018 ( 21) link_BETA1-4 : angle 3.50489 ( 63) link_ALPHA1-3 : bond 0.02099 ( 1) link_ALPHA1-3 : angle 2.38693 ( 3) hydrogen bonds : bond 0.03959 ( 186) hydrogen bonds : angle 6.57833 ( 489) link_BETA1-6 : bond 0.01045 ( 1) link_BETA1-6 : angle 1.96072 ( 3) SS BOND : bond 0.00288 ( 15) SS BOND : angle 0.63844 ( 30) covalent geometry : bond 0.00294 ( 9023) covalent geometry : angle 0.67809 (12285) *********************** 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 136 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6489 (Cg_endo) cc_final: 0.6284 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6221 (m-80) cc_final: 0.6014 (m-80) REVERT: A 272 PHE cc_start: 0.4141 (OUTLIER) cc_final: 0.3577 (m-80) REVERT: A 277 THR cc_start: 0.7447 (p) cc_final: 0.7077 (t) REVERT: A 328 ASN cc_start: 0.3470 (OUTLIER) cc_final: 0.2614 (m110) REVERT: A 434 VAL cc_start: 0.8191 (m) cc_final: 0.7683 (t) REVERT: A 454 LYS cc_start: 0.7501 (tppt) cc_final: 0.7228 (tttt) REVERT: A 548 ASN cc_start: 0.6152 (m-40) cc_final: 0.5325 (m110) REVERT: A 622 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.4888 (tp) outliers start: 30 outliers final: 11 residues processed: 126 average time/residue: 0.7694 time to fit residues: 107.1637 Evaluate side-chains 117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 0.0010 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 647 HIS C 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.254928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.227697 restraints weight = 13921.687| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 3.05 r_work: 0.4579 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.2767 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= 0.167 Angle : 0.759 13.336 12438 Z= 0.337 Chirality : 0.052 0.568 1458 Planarity : 0.004 0.058 1560 Dihedral : 11.312 70.015 1989 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.52 % Favored : 92.11 % Rotamer: Outliers : 3.16 % Allowed : 10.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1064 helix: 1.70 (0.78), residues: 54 sheet: 0.12 (0.31), residues: 275 loop : -0.93 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 819 HIS 0.007 0.001 HIS D 844 PHE 0.022 0.002 PHE A 568 TYR 0.018 0.002 TYR D 868 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 16) link_NAG-ASN : angle 3.38055 ( 48) link_ALPHA1-6 : bond 0.00298 ( 2) link_ALPHA1-6 : angle 1.91018 ( 6) link_BETA1-4 : bond 0.01003 ( 21) link_BETA1-4 : angle 3.45027 ( 63) link_ALPHA1-3 : bond 0.02271 ( 1) link_ALPHA1-3 : angle 2.42469 ( 3) hydrogen bonds : bond 0.03841 ( 186) hydrogen bonds : angle 6.26322 ( 489) link_BETA1-6 : bond 0.00991 ( 1) link_BETA1-6 : angle 1.95538 ( 3) SS BOND : bond 0.00342 ( 15) SS BOND : angle 0.80524 ( 30) covalent geometry : bond 0.00346 ( 9023) covalent geometry : angle 0.68658 (12285) *********************** 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: 29 poor density : 103 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6658 (Cg_endo) cc_final: 0.6438 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5133 (pt) REVERT: D 976 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.4982 (mtt) REVERT: D 1004 TYR cc_start: 0.7116 (m-10) cc_final: 0.6875 (m-10) REVERT: D 1017 PHE cc_start: 0.6370 (m-80) cc_final: 0.6116 (m-80) REVERT: A 272 PHE cc_start: 0.4295 (OUTLIER) cc_final: 0.3777 (m-80) REVERT: A 277 THR cc_start: 0.7635 (p) cc_final: 0.7272 (t) REVERT: A 316 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6669 (tm) REVERT: A 328 ASN cc_start: 0.3272 (OUTLIER) cc_final: 0.2999 (m110) REVERT: A 357 VAL cc_start: 0.6209 (OUTLIER) cc_final: 0.5941 (t) REVERT: A 364 ASN cc_start: 0.6551 (p0) cc_final: 0.6325 (p0) REVERT: A 528 PHE cc_start: 0.5108 (OUTLIER) cc_final: 0.4833 (m-10) outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 0.7750 time to fit residues: 103.5594 Evaluate side-chains 119 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 528 PHE Chi-restraints excluded: chain A residue 564 ILE 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 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 875 ASN A 463 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.257454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.230681 restraints weight = 14089.563| |-----------------------------------------------------------------------------| r_work (start): 0.4699 rms_B_bonded: 3.03 r_work: 0.4595 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.2866 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= 0.123 Angle : 0.709 13.485 12438 Z= 0.311 Chirality : 0.050 0.560 1458 Planarity : 0.004 0.049 1560 Dihedral : 10.475 71.851 1989 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.02 % Favored : 93.61 % Rotamer: Outliers : 3.49 % Allowed : 10.25 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1064 helix: 1.63 (0.77), residues: 54 sheet: 0.18 (0.31), residues: 275 loop : -0.93 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 819 HIS 0.008 0.001 HIS C 63 PHE 0.030 0.002 PHE A 374 TYR 0.013 0.001 TYR D1004 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 16) link_NAG-ASN : angle 3.53536 ( 48) link_ALPHA1-6 : bond 0.00350 ( 2) link_ALPHA1-6 : angle 1.59575 ( 6) link_BETA1-4 : bond 0.00991 ( 21) link_BETA1-4 : angle 3.30920 ( 63) link_ALPHA1-3 : bond 0.02294 ( 1) link_ALPHA1-3 : angle 2.51143 ( 3) hydrogen bonds : bond 0.03082 ( 186) hydrogen bonds : angle 6.15205 ( 489) link_BETA1-6 : bond 0.01079 ( 1) link_BETA1-6 : angle 1.96871 ( 3) SS BOND : bond 0.00235 ( 15) SS BOND : angle 0.60194 ( 30) covalent geometry : bond 0.00256 ( 9023) covalent geometry : angle 0.63137 (12285) *********************** 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 129 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6524 (Cg_endo) cc_final: 0.6305 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.5183 (pt) REVERT: D 976 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.5015 (mtt) REVERT: D 1017 PHE cc_start: 0.6330 (m-80) cc_final: 0.6098 (m-80) REVERT: A 261 GLN cc_start: 0.5687 (tp40) cc_final: 0.5417 (tp40) REVERT: A 272 PHE cc_start: 0.4246 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: A 316 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6695 (tm) REVERT: A 328 ASN cc_start: 0.3378 (OUTLIER) cc_final: 0.2899 (m110) REVERT: A 528 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4798 (m-10) REVERT: A 622 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4800 (tp) outliers start: 32 outliers final: 15 residues processed: 115 average time/residue: 0.7646 time to fit residues: 97.5439 Evaluate side-chains 116 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 875 ASN 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 405 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 574 GLU 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 Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1015 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.254282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.227048 restraints weight = 13667.740| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 3.02 r_work: 0.4564 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.3237 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= 0.182 Angle : 0.765 13.455 12438 Z= 0.346 Chirality : 0.052 0.568 1458 Planarity : 0.004 0.058 1560 Dihedral : 10.303 68.317 1989 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.99 % Favored : 91.64 % Rotamer: Outliers : 4.58 % Allowed : 10.47 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1064 helix: 1.58 (0.79), residues: 54 sheet: -0.09 (0.31), residues: 285 loop : -1.08 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 819 HIS 0.006 0.002 HIS D 844 PHE 0.025 0.002 PHE A 568 TYR 0.022 0.002 TYR D 868 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 16) link_NAG-ASN : angle 3.48880 ( 48) link_ALPHA1-6 : bond 0.00278 ( 2) link_ALPHA1-6 : angle 1.72140 ( 6) link_BETA1-4 : bond 0.00983 ( 21) link_BETA1-4 : angle 3.32798 ( 63) link_ALPHA1-3 : bond 0.02261 ( 1) link_ALPHA1-3 : angle 2.31152 ( 3) hydrogen bonds : bond 0.03631 ( 186) hydrogen bonds : angle 6.45742 ( 489) link_BETA1-6 : bond 0.00896 ( 1) link_BETA1-6 : angle 1.89643 ( 3) SS BOND : bond 0.00312 ( 15) SS BOND : angle 1.33452 ( 30) covalent geometry : bond 0.00385 ( 9023) covalent geometry : angle 0.69272 (12285) *********************** 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 139 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 0.947 Fit side-chains REVERT: D 906 PRO cc_start: 0.6682 (Cg_endo) cc_final: 0.6469 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6319 (OUTLIER) cc_final: 0.5227 (pt) REVERT: D 976 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5305 (mtt) REVERT: D 1017 PHE cc_start: 0.6425 (m-80) cc_final: 0.6168 (m-80) REVERT: A 261 GLN cc_start: 0.5786 (tp40) cc_final: 0.5566 (tp40) REVERT: A 272 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3787 (m-80) REVERT: A 277 THR cc_start: 0.7575 (p) cc_final: 0.7202 (t) REVERT: A 316 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6776 (tm) REVERT: A 328 ASN cc_start: 0.3396 (OUTLIER) cc_final: 0.2962 (m110) REVERT: A 370 GLN cc_start: 0.6381 (mp10) cc_final: 0.6098 (mp10) REVERT: A 622 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5396 (tt) outliers start: 42 outliers final: 23 residues processed: 120 average time/residue: 0.8680 time to fit residues: 115.7753 Evaluate side-chains 125 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 342 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER 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 45 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.252074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.225771 restraints weight = 13789.734| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 2.98 r_work: 0.4560 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.3464 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= 0.165 Angle : 0.752 13.196 12438 Z= 0.339 Chirality : 0.052 0.555 1458 Planarity : 0.004 0.053 1560 Dihedral : 10.015 72.416 1989 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.95 % Favored : 92.67 % Rotamer: Outliers : 3.93 % Allowed : 11.12 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1064 helix: 1.44 (0.78), residues: 54 sheet: -0.25 (0.31), residues: 285 loop : -1.16 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 819 HIS 0.005 0.001 HIS C 96 PHE 0.020 0.002 PHE A 606 TYR 0.024 0.002 TYR A 427 ARG 0.007 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 16) link_NAG-ASN : angle 3.47438 ( 48) link_ALPHA1-6 : bond 0.00311 ( 2) link_ALPHA1-6 : angle 1.61162 ( 6) link_BETA1-4 : bond 0.00970 ( 21) link_BETA1-4 : angle 3.29250 ( 63) link_ALPHA1-3 : bond 0.02115 ( 1) link_ALPHA1-3 : angle 2.25122 ( 3) hydrogen bonds : bond 0.03417 ( 186) hydrogen bonds : angle 6.38868 ( 489) link_BETA1-6 : bond 0.00935 ( 1) link_BETA1-6 : angle 1.91400 ( 3) SS BOND : bond 0.00355 ( 15) SS BOND : angle 1.14664 ( 30) covalent geometry : bond 0.00351 ( 9023) covalent geometry : angle 0.68112 (12285) *********************** 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: 36 poor density : 102 time to evaluate : 0.820 Fit side-chains REVERT: D 906 PRO cc_start: 0.6712 (Cg_endo) cc_final: 0.6499 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.5176 (pt) REVERT: D 1017 PHE cc_start: 0.6574 (m-80) cc_final: 0.6291 (m-80) REVERT: A 261 GLN cc_start: 0.5741 (tp40) cc_final: 0.5513 (tp40) REVERT: A 272 PHE cc_start: 0.4255 (OUTLIER) cc_final: 0.3789 (m-80) REVERT: A 277 THR cc_start: 0.7529 (p) cc_final: 0.7152 (t) REVERT: A 316 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6723 (tm) REVERT: A 328 ASN cc_start: 0.3330 (OUTLIER) cc_final: 0.2930 (m-40) REVERT: A 622 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5355 (tt) outliers start: 36 outliers final: 19 residues processed: 121 average time/residue: 0.8110 time to fit residues: 108.5946 Evaluate side-chains 123 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 342 TYR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 605 VAL 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 Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 466 GLN C 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.252286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.225366 restraints weight = 13954.619| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 3.09 r_work: 0.4558 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9079 Z= 0.158 Angle : 0.757 13.218 12438 Z= 0.339 Chirality : 0.051 0.560 1458 Planarity : 0.004 0.073 1560 Dihedral : 9.867 70.428 1989 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.89 % Favored : 91.73 % Rotamer: Outliers : 3.82 % Allowed : 11.67 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1064 helix: 1.44 (0.78), residues: 54 sheet: -0.39 (0.31), residues: 277 loop : -1.16 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 819 HIS 0.005 0.001 HIS A 384 PHE 0.019 0.002 PHE A 452 TYR 0.016 0.002 TYR D 868 ARG 0.007 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 16) link_NAG-ASN : angle 3.80826 ( 48) link_ALPHA1-6 : bond 0.00288 ( 2) link_ALPHA1-6 : angle 1.58787 ( 6) link_BETA1-4 : bond 0.00997 ( 21) link_BETA1-4 : angle 3.30790 ( 63) link_ALPHA1-3 : bond 0.01998 ( 1) link_ALPHA1-3 : angle 2.17397 ( 3) hydrogen bonds : bond 0.03455 ( 186) hydrogen bonds : angle 6.41322 ( 489) link_BETA1-6 : bond 0.00935 ( 1) link_BETA1-6 : angle 1.90882 ( 3) SS BOND : bond 0.00356 ( 15) SS BOND : angle 1.20134 ( 30) covalent geometry : bond 0.00334 ( 9023) covalent geometry : angle 0.67829 (12285) *********************** 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 134 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.792 Fit side-chains REVERT: D 955 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5238 (pt) REVERT: D 1017 PHE cc_start: 0.6691 (m-80) cc_final: 0.6387 (m-80) REVERT: A 261 GLN cc_start: 0.5733 (tp40) cc_final: 0.5512 (tp40) REVERT: A 272 PHE cc_start: 0.4250 (OUTLIER) cc_final: 0.3769 (m-80) REVERT: A 277 THR cc_start: 0.7502 (p) cc_final: 0.7127 (t) REVERT: A 316 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6710 (tm) REVERT: A 328 ASN cc_start: 0.3374 (OUTLIER) cc_final: 0.3020 (m-40) outliers start: 35 outliers final: 23 residues processed: 121 average time/residue: 0.7987 time to fit residues: 107.1318 Evaluate side-chains 124 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 405 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 566 LEU 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 Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.2980 chunk 75 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 21 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.254321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.228052 restraints weight = 14029.164| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 3.02 r_work: 0.4586 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9079 Z= 0.118 Angle : 0.723 12.991 12438 Z= 0.322 Chirality : 0.050 0.551 1458 Planarity : 0.004 0.059 1560 Dihedral : 9.424 74.428 1989 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.77 % Favored : 92.86 % Rotamer: Outliers : 3.16 % Allowed : 12.32 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1064 helix: 1.42 (0.76), residues: 54 sheet: -0.40 (0.31), residues: 287 loop : -1.10 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 819 HIS 0.004 0.001 HIS C 63 PHE 0.052 0.002 PHE A 374 TYR 0.012 0.001 TYR D1004 ARG 0.008 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 16) link_NAG-ASN : angle 3.56018 ( 48) link_ALPHA1-6 : bond 0.00385 ( 2) link_ALPHA1-6 : angle 1.47252 ( 6) link_BETA1-4 : bond 0.00960 ( 21) link_BETA1-4 : angle 3.18179 ( 63) link_ALPHA1-3 : bond 0.01862 ( 1) link_ALPHA1-3 : angle 2.19566 ( 3) hydrogen bonds : bond 0.03044 ( 186) hydrogen bonds : angle 6.20620 ( 489) link_BETA1-6 : bond 0.01048 ( 1) link_BETA1-6 : angle 1.91267 ( 3) SS BOND : bond 0.00293 ( 15) SS BOND : angle 0.96709 ( 30) covalent geometry : bond 0.00244 ( 9023) covalent geometry : angle 0.65009 (12285) *********************** 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 126 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.880 Fit side-chains REVERT: D 955 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5175 (pt) REVERT: D 1017 PHE cc_start: 0.6596 (m-80) cc_final: 0.6326 (m-80) REVERT: A 261 GLN cc_start: 0.5749 (tp40) cc_final: 0.5537 (tp40) REVERT: A 272 PHE cc_start: 0.4175 (OUTLIER) cc_final: 0.3704 (m-80) REVERT: A 277 THR cc_start: 0.7308 (p) cc_final: 0.6943 (t) REVERT: A 316 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6727 (tm) REVERT: A 328 ASN cc_start: 0.3293 (OUTLIER) cc_final: 0.3028 (m-40) REVERT: A 454 LYS cc_start: 0.7265 (tppt) cc_final: 0.7016 (tttt) REVERT: A 611 ARG cc_start: 0.7866 (ttt-90) cc_final: 0.7557 (tmt-80) outliers start: 29 outliers final: 20 residues processed: 116 average time/residue: 0.8045 time to fit residues: 102.9418 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 : 0.861 ------------------------------------------------------------------------------- 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 885 LYS 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 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 405 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 566 LEU 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 Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** C 76 HIS ** 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 = 0.4913 r_free = 0.4913 target = 0.252512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.226054 restraints weight = 13755.191| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 2.98 r_work: 0.4563 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9079 Z= 0.157 Angle : 0.752 12.970 12438 Z= 0.338 Chirality : 0.051 0.555 1458 Planarity : 0.004 0.069 1560 Dihedral : 9.432 69.822 1989 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.18 % Favored : 91.45 % Rotamer: Outliers : 2.73 % Allowed : 13.85 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 1064 helix: 1.44 (0.78), residues: 54 sheet: -0.42 (0.31), residues: 277 loop : -1.17 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 819 HIS 0.008 0.001 HIS C 63 PHE 0.034 0.002 PHE A 374 TYR 0.015 0.001 TYR D 868 ARG 0.008 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 16) link_NAG-ASN : angle 3.56634 ( 48) link_ALPHA1-6 : bond 0.00286 ( 2) link_ALPHA1-6 : angle 1.59060 ( 6) link_BETA1-4 : bond 0.00985 ( 21) link_BETA1-4 : angle 3.21458 ( 63) link_ALPHA1-3 : bond 0.01842 ( 1) link_ALPHA1-3 : angle 2.15846 ( 3) hydrogen bonds : bond 0.03377 ( 186) hydrogen bonds : angle 6.24643 ( 489) link_BETA1-6 : bond 0.00904 ( 1) link_BETA1-6 : angle 1.84608 ( 3) SS BOND : bond 0.00342 ( 15) SS BOND : angle 1.05263 ( 30) covalent geometry : bond 0.00332 ( 9023) covalent geometry : angle 0.68125 (12285) ********************** 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 125 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: D 955 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.5160 (pt) REVERT: D 1017 PHE cc_start: 0.6694 (m-80) cc_final: 0.6396 (m-80) REVERT: A 261 GLN cc_start: 0.5770 (tp40) cc_final: 0.5556 (tp40) REVERT: A 272 PHE cc_start: 0.4177 (OUTLIER) cc_final: 0.3729 (m-80) REVERT: A 277 THR cc_start: 0.7444 (p) cc_final: 0.7075 (t) REVERT: A 316 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6775 (tm) REVERT: A 328 ASN cc_start: 0.3345 (OUTLIER) cc_final: 0.3072 (m-40) REVERT: A 632 THR cc_start: 0.5728 (m) cc_final: 0.5510 (p) REVERT: A 717 GLN cc_start: 0.6491 (tt0) cc_final: 0.6291 (tt0) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.8180 time to fit residues: 105.8823 Evaluate side-chains 120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 566 LEU 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 Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 0.0970 chunk 85 optimal weight: 0.2980 chunk 26 optimal weight: 0.1980 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 91 optimal weight: 0.0870 chunk 38 optimal weight: 0.0170 chunk 73 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.1394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.255289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.229499 restraints weight = 13977.640| |-----------------------------------------------------------------------------| r_work (start): 0.4705 rms_B_bonded: 2.99 r_work: 0.4605 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 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 : 0.002 0.038 9079 Z= 0.114 Angle : 0.705 12.876 12438 Z= 0.316 Chirality : 0.049 0.546 1458 Planarity : 0.004 0.059 1560 Dihedral : 9.045 72.874 1989 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.58 % Favored : 93.05 % Rotamer: Outliers : 2.18 % Allowed : 14.18 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1064 helix: 1.39 (0.76), residues: 54 sheet: -0.40 (0.31), residues: 287 loop : -1.12 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 819 HIS 0.003 0.001 HIS C 63 PHE 0.033 0.002 PHE A 374 TYR 0.013 0.001 TYR D1004 ARG 0.007 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 16) link_NAG-ASN : angle 3.38587 ( 48) link_ALPHA1-6 : bond 0.00451 ( 2) link_ALPHA1-6 : angle 1.45119 ( 6) link_BETA1-4 : bond 0.01027 ( 21) link_BETA1-4 : angle 3.12343 ( 63) link_ALPHA1-3 : bond 0.01858 ( 1) link_ALPHA1-3 : angle 2.15822 ( 3) hydrogen bonds : bond 0.02878 ( 186) hydrogen bonds : angle 6.12082 ( 489) link_BETA1-6 : bond 0.01034 ( 1) link_BETA1-6 : angle 1.85144 ( 3) SS BOND : bond 0.00283 ( 15) SS BOND : angle 0.88664 ( 30) covalent geometry : bond 0.00233 ( 9023) covalent geometry : angle 0.63478 (12285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6240.53 seconds wall clock time: 108 minutes 36.37 seconds (6516.37 seconds total)