Starting phenix.real_space_refine on Sat Jun 7 14:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi4_60121/06_2025/8zi4_60121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi4_60121/06_2025/8zi4_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/8zi4_60121/06_2025/8zi4_60121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi4_60121/06_2025/8zi4_60121.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi4_60121/06_2025/8zi4_60121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi4_60121/06_2025/8zi4_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: "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: "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: "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: 5.79, per 1000 atoms: 0.66 Number of scatterers: 8818 At special positions: 0 Unit cell: (83.88, 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=16, symmetry=0 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 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 185 " distance=2.03 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 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: 2.85 Conformation dependent library (CDL) restraints added in 1.0 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, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.705A pdb=" N TYR C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 removed outlier: 4.206A pdb=" N THR C 242 " --> pdb=" O TRP C 238 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.520A pdb=" N VAL C 39 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 48 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 92 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 162 removed outlier: 6.940A pdb=" N VAL C 204 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL C 214 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR C 230 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, 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=AA5, 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=AA6, 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=AA7, 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=AA8, 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=AA9, 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=AB1, 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=AB2, first strand: chain 'A' and resid 442 through 443 Processing sheet with id=AB3, 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=AB4, first strand: chain 'A' and resid 563 through 565 Processing sheet with id=AB5, 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=AB6, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AB7, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AB8, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AB9, 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) 192 hydrogen bonds defined for protein. 483 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: 2.83 Time building geometry restraints manager: 3.26 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: 2265 1.42 - 1.55: 5222 1.55 - 1.68: 7 1.68 - 1.82: 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: 12028 2.45 - 4.90: 195 4.90 - 7.34: 52 7.34 - 9.79: 8 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=" O PHE A 327 " pdb=" C PHE A 327 " pdb=" N ASN A 328 " ideal model delta sigma weight residual 123.27 131.75 -8.48 1.22e+00 6.72e-01 4.83e+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=" CA PHE A 327 " pdb=" C PHE A 327 " pdb=" N ASN A 328 " ideal model delta sigma weight residual 116.00 108.10 7.90 1.50e+00 4.44e-01 2.77e+01 ... (remaining 12280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 5621 23.70 - 47.41: 113 47.41 - 71.11: 35 71.11 - 94.81: 72 94.81 - 118.52: 45 Dihedral angle restraints: 5886 sinusoidal: 2829 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 5883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 1431 0.153 - 0.306: 23 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: 1.99 - 2.57: 90 2.57 - 3.15: 7017 3.15 - 3.74: 13009 3.74 - 4.32: 18098 4.32 - 4.90: 29821 Nonbonded interactions: 68035 Sorted by model distance: nonbonded pdb=" O4 NAG A 802 " pdb=" O6 NAG A 802 " model vdw 1.991 3.040 nonbonded pdb=" O3 NAG A 802 " pdb=" O7 NAG A 802 " model vdw 2.049 3.040 nonbonded pdb=" O ASN D 981 " pdb=" ND2 ASN D 981 " model vdw 2.085 3.120 nonbonded pdb=" O3 NAG G 1 " pdb=" O7 NAG G 1 " model vdw 2.124 3.040 nonbonded pdb=" O3 NAG A 803 " pdb=" O7 NAG A 803 " model vdw 2.127 3.040 ... (remaining 68030 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: 1.280 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.040 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5197 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 9080 Z= 0.231 Angle : 0.858 20.593 12440 Z= 0.378 Chirality : 0.061 0.766 1458 Planarity : 0.009 0.269 1560 Dihedral : 18.350 118.518 3886 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.39 % Favored : 93.05 % Rotamer: Outliers : 1.85 % Allowed : 3.60 % Favored : 94.55 % 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: -0.15 (0.27), residues: 1064 helix: 0.90 (0.77), residues: 56 sheet: 0.67 (0.33), residues: 277 loop : -0.49 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 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 0.25220 ( 184) hydrogen bonds : angle 10.42144 ( 483) link_BETA1-6 : bond 0.00683 ( 1) link_BETA1-6 : angle 1.27728 ( 3) SS BOND : bond 0.00123 ( 16) SS BOND : angle 0.49932 ( 32) covalent geometry : bond 0.00429 ( 9023) covalent geometry : angle 0.75077 (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 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.3932 (OUTLIER) cc_final: 0.3427 (m-80) REVERT: A 295 SER cc_start: 0.6104 (t) cc_final: 0.5889 (p) REVERT: A 548 ASN cc_start: 0.5722 (m-40) cc_final: 0.4854 (m-40) REVERT: A 619 ASN cc_start: 0.4427 (OUTLIER) cc_final: 0.3335 (p0) REVERT: A 622 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4959 (tp) outliers start: 17 outliers final: 8 residues processed: 136 average time/residue: 0.7493 time to fit residues: 112.9873 Evaluate side-chains 121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN C 159 GLN C 222 GLN D 844 HIS D 881 HIS D 921 GLN D 929 GLN A 310 GLN A 358 GLN A 435 HIS A 619 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS A 768 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.259909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.234868 restraints weight = 14089.128| |-----------------------------------------------------------------------------| r_work (start): 0.4746 rms_B_bonded: 2.97 r_work: 0.4644 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5283 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9080 Z= 0.137 Angle : 0.776 13.283 12440 Z= 0.337 Chirality : 0.052 0.570 1458 Planarity : 0.004 0.041 1560 Dihedral : 17.504 89.947 1998 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.30 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 8.51 % Favored : 89.42 % 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: -0.33 (0.27), residues: 1064 helix: 0.68 (0.74), residues: 60 sheet: 0.47 (0.33), residues: 275 loop : -0.58 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 819 HIS 0.004 0.001 HIS D 881 PHE 0.023 0.002 PHE A 568 TYR 0.015 0.001 TYR C 45 ARG 0.007 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 16) link_NAG-ASN : angle 3.66331 ( 48) link_ALPHA1-6 : bond 0.00236 ( 2) link_ALPHA1-6 : angle 1.93074 ( 6) link_BETA1-4 : bond 0.01024 ( 21) link_BETA1-4 : angle 3.64988 ( 63) link_ALPHA1-3 : bond 0.01574 ( 1) link_ALPHA1-3 : angle 2.47475 ( 3) hydrogen bonds : bond 0.04643 ( 184) hydrogen bonds : angle 7.49382 ( 483) link_BETA1-6 : bond 0.01235 ( 1) link_BETA1-6 : angle 2.16047 ( 3) SS BOND : bond 0.00301 ( 16) SS BOND : angle 1.00441 ( 32) covalent geometry : bond 0.00279 ( 9023) covalent geometry : angle 0.69374 (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 123 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 945 MET cc_start: 0.5962 (mtm) cc_final: 0.5316 (ttt) REVERT: A 272 PHE cc_start: 0.3954 (OUTLIER) cc_final: 0.3454 (m-80) REVERT: A 277 THR cc_start: 0.7240 (p) cc_final: 0.6866 (t) REVERT: A 328 ASN cc_start: 0.3415 (OUTLIER) cc_final: 0.2874 (m110) REVERT: A 548 ASN cc_start: 0.5828 (m-40) cc_final: 0.5230 (m-40) REVERT: A 622 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4878 (tp) REVERT: A 682 ASN cc_start: 0.2067 (OUTLIER) cc_final: 0.1721 (p0) outliers start: 19 outliers final: 7 residues processed: 120 average time/residue: 0.8196 time to fit residues: 108.4945 Evaluate side-chains 115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 863 VAL 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 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 622 LEU Chi-restraints excluded: chain A residue 682 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.257376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.231288 restraints weight = 14153.267| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 3.05 r_work: 0.4610 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9080 Z= 0.149 Angle : 0.757 13.344 12440 Z= 0.331 Chirality : 0.052 0.561 1458 Planarity : 0.004 0.043 1560 Dihedral : 14.034 78.057 1994 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.24 % Favored : 92.39 % Rotamer: Outliers : 2.40 % Allowed : 9.92 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.27), residues: 1064 helix: 0.68 (0.76), residues: 60 sheet: 0.21 (0.32), residues: 269 loop : -0.66 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 819 HIS 0.006 0.001 HIS D 844 PHE 0.017 0.002 PHE A 568 TYR 0.017 0.001 TYR C 175 ARG 0.007 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 16) link_NAG-ASN : angle 3.44668 ( 48) link_ALPHA1-6 : bond 0.00281 ( 2) link_ALPHA1-6 : angle 1.91072 ( 6) link_BETA1-4 : bond 0.01019 ( 21) link_BETA1-4 : angle 3.50939 ( 63) link_ALPHA1-3 : bond 0.02269 ( 1) link_ALPHA1-3 : angle 2.46280 ( 3) hydrogen bonds : bond 0.03941 ( 184) hydrogen bonds : angle 6.86722 ( 483) link_BETA1-6 : bond 0.01074 ( 1) link_BETA1-6 : angle 1.98973 ( 3) SS BOND : bond 0.00991 ( 16) SS BOND : angle 0.79277 ( 32) covalent geometry : bond 0.00299 ( 9023) covalent geometry : angle 0.68164 (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 125 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6520 (Cg_endo) cc_final: 0.6318 (Cg_exo) REVERT: D 954 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6188 (mtm) REVERT: D 1017 PHE cc_start: 0.6287 (m-80) cc_final: 0.6040 (m-80) REVERT: A 272 PHE cc_start: 0.3934 (OUTLIER) cc_final: 0.3632 (m-80) REVERT: A 277 THR cc_start: 0.7492 (p) cc_final: 0.7119 (t) REVERT: A 324 TYR cc_start: 0.5576 (t80) cc_final: 0.5284 (t80) REVERT: A 328 ASN cc_start: 0.3421 (OUTLIER) cc_final: 0.2989 (m110) outliers start: 22 outliers final: 9 residues processed: 119 average time/residue: 0.7954 time to fit residues: 104.3540 Evaluate side-chains 110 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 VAL Chi-restraints excluded: chain D residue 871 ARG Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 954 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 306 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 574 GLU Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1015 GLN A 466 GLN A 647 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.255209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.229203 restraints weight = 13911.525| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 2.98 r_work: 0.4589 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5449 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9080 Z= 0.170 Angle : 0.764 13.237 12440 Z= 0.342 Chirality : 0.052 0.562 1458 Planarity : 0.004 0.054 1560 Dihedral : 11.500 70.480 1989 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.52 % Favored : 92.11 % Rotamer: Outliers : 3.05 % Allowed : 10.69 % 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: -0.83 (0.26), residues: 1064 helix: 0.56 (0.76), residues: 60 sheet: -0.15 (0.31), residues: 274 loop : -0.83 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 819 HIS 0.007 0.001 HIS D 844 PHE 0.026 0.002 PHE A 568 TYR 0.017 0.002 TYR D 868 ARG 0.005 0.001 ARG A 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 16) link_NAG-ASN : angle 3.37875 ( 48) link_ALPHA1-6 : bond 0.00265 ( 2) link_ALPHA1-6 : angle 1.89548 ( 6) link_BETA1-4 : bond 0.01018 ( 21) link_BETA1-4 : angle 3.46153 ( 63) link_ALPHA1-3 : bond 0.02327 ( 1) link_ALPHA1-3 : angle 2.39418 ( 3) hydrogen bonds : bond 0.03831 ( 184) hydrogen bonds : angle 6.58242 ( 483) link_BETA1-6 : bond 0.01001 ( 1) link_BETA1-6 : angle 1.93080 ( 3) SS BOND : bond 0.00381 ( 16) SS BOND : angle 0.96081 ( 32) covalent geometry : bond 0.00350 ( 9023) covalent geometry : angle 0.69136 (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 133 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6630 (Cg_endo) cc_final: 0.6411 (Cg_exo) REVERT: D 954 MET cc_start: 0.6533 (mtm) cc_final: 0.6273 (mtm) REVERT: D 955 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5058 (pt) REVERT: D 976 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.4958 (mtt) REVERT: D 1017 PHE cc_start: 0.6448 (m-80) cc_final: 0.6166 (m-80) REVERT: A 272 PHE cc_start: 0.4204 (OUTLIER) cc_final: 0.3698 (m-80) REVERT: A 277 THR cc_start: 0.7585 (p) cc_final: 0.7239 (t) REVERT: A 316 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6675 (tm) REVERT: A 328 ASN cc_start: 0.3579 (OUTLIER) cc_final: 0.3165 (m110) REVERT: A 357 VAL cc_start: 0.6203 (OUTLIER) cc_final: 0.5518 (m) outliers start: 28 outliers final: 14 residues processed: 122 average time/residue: 0.8116 time to fit residues: 110.3171 Evaluate side-chains 123 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 871 ARG 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 976 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.255054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.228842 restraints weight = 13838.903| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 2.95 r_work: 0.4586 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9080 Z= 0.154 Angle : 0.735 13.105 12440 Z= 0.330 Chirality : 0.051 0.561 1458 Planarity : 0.004 0.047 1560 Dihedral : 10.674 69.732 1989 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.52 % Favored : 92.11 % Rotamer: Outliers : 3.49 % Allowed : 11.56 % 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: -0.98 (0.26), residues: 1064 helix: 0.62 (0.78), residues: 54 sheet: -0.33 (0.31), residues: 278 loop : -0.90 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 819 HIS 0.006 0.001 HIS C 63 PHE 0.039 0.002 PHE A 568 TYR 0.015 0.001 TYR A 324 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 16) link_NAG-ASN : angle 3.37339 ( 48) link_ALPHA1-6 : bond 0.00262 ( 2) link_ALPHA1-6 : angle 1.68773 ( 6) link_BETA1-4 : bond 0.00986 ( 21) link_BETA1-4 : angle 3.34215 ( 63) link_ALPHA1-3 : bond 0.02322 ( 1) link_ALPHA1-3 : angle 2.34614 ( 3) hydrogen bonds : bond 0.03503 ( 184) hydrogen bonds : angle 6.73582 ( 483) link_BETA1-6 : bond 0.00984 ( 1) link_BETA1-6 : angle 1.92888 ( 3) SS BOND : bond 0.00355 ( 16) SS BOND : angle 1.33684 ( 32) covalent geometry : bond 0.00327 ( 9023) covalent geometry : angle 0.66073 (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 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6626 (Cg_endo) cc_final: 0.6413 (Cg_exo) REVERT: D 954 MET cc_start: 0.6302 (mtm) cc_final: 0.6070 (mtt) REVERT: D 955 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.4971 (pt) REVERT: D 976 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.5460 (ptt) REVERT: D 1004 TYR cc_start: 0.7076 (m-10) cc_final: 0.6864 (m-10) REVERT: D 1017 PHE cc_start: 0.6528 (m-80) cc_final: 0.6227 (m-80) REVERT: A 272 PHE cc_start: 0.4227 (OUTLIER) cc_final: 0.3704 (m-80) REVERT: A 277 THR cc_start: 0.7504 (p) cc_final: 0.7153 (t) REVERT: A 316 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6695 (tm) REVERT: A 328 ASN cc_start: 0.3557 (OUTLIER) cc_final: 0.3133 (m110) REVERT: A 434 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8087 (m) REVERT: A 528 PHE cc_start: 0.5049 (OUTLIER) cc_final: 0.4739 (m-10) REVERT: A 622 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5159 (tt) outliers start: 32 outliers final: 13 residues processed: 129 average time/residue: 0.7804 time to fit residues: 111.4170 Evaluate side-chains 130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 442 SER Chi-restraints excluded: chain A residue 447 MET 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 A residue 691 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 953 ASN A 209 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.246580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.220363 restraints weight = 13201.261| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 2.85 r_work: 0.4510 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 9080 Z= 0.370 Angle : 0.969 13.088 12440 Z= 0.466 Chirality : 0.060 0.581 1458 Planarity : 0.006 0.068 1560 Dihedral : 11.269 67.776 1985 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.62 % Favored : 89.00 % Rotamer: Outliers : 4.69 % Allowed : 10.80 % Favored : 84.51 % 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: -1.70 (0.25), residues: 1064 helix: -0.69 (0.70), residues: 61 sheet: -0.66 (0.31), residues: 278 loop : -1.43 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP D 819 HIS 0.016 0.003 HIS D 844 PHE 0.041 0.003 PHE A 374 TYR 0.050 0.003 TYR D 868 ARG 0.011 0.001 ARG D 871 Details of bonding type rmsd link_NAG-ASN : bond 0.00924 ( 16) link_NAG-ASN : angle 4.13279 ( 48) link_ALPHA1-6 : bond 0.00226 ( 2) link_ALPHA1-6 : angle 2.13993 ( 6) link_BETA1-4 : bond 0.00999 ( 21) link_BETA1-4 : angle 3.51612 ( 63) link_ALPHA1-3 : bond 0.02550 ( 1) link_ALPHA1-3 : angle 2.05880 ( 3) hydrogen bonds : bond 0.05598 ( 184) hydrogen bonds : angle 7.24447 ( 483) link_BETA1-6 : bond 0.00579 ( 1) link_BETA1-6 : angle 1.87244 ( 3) SS BOND : bond 0.00713 ( 16) SS BOND : angle 1.75461 ( 32) covalent geometry : bond 0.00769 ( 9023) covalent geometry : angle 0.89946 (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 153 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.814 Fit side-chains REVERT: D 955 ILE cc_start: 0.6349 (OUTLIER) cc_final: 0.5195 (pt) REVERT: D 1017 PHE cc_start: 0.6835 (m-80) cc_final: 0.6492 (m-80) REVERT: A 272 PHE cc_start: 0.4496 (OUTLIER) cc_final: 0.4004 (m-80) REVERT: A 316 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6729 (tm) REVERT: A 324 TYR cc_start: 0.6308 (t80) cc_final: 0.6020 (t80) REVERT: A 328 ASN cc_start: 0.3564 (OUTLIER) cc_final: 0.3299 (m-40) REVERT: A 483 LYS cc_start: 0.6615 (tttm) cc_final: 0.6369 (tttm) REVERT: A 566 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6348 (pp) outliers start: 43 outliers final: 16 residues processed: 136 average time/residue: 0.7294 time to fit residues: 110.2245 Evaluate side-chains 131 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 TYR 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 945 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.251485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.225199 restraints weight = 13688.592| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 2.97 r_work: 0.4552 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9080 Z= 0.155 Angle : 0.773 13.162 12440 Z= 0.354 Chirality : 0.052 0.554 1458 Planarity : 0.005 0.059 1560 Dihedral : 10.292 73.109 1985 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.86 % Favored : 92.76 % Rotamer: Outliers : 3.49 % Allowed : 12.54 % Favored : 83.97 % 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: -1.64 (0.25), residues: 1064 helix: 0.14 (0.78), residues: 55 sheet: -0.89 (0.31), residues: 278 loop : -1.31 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 819 HIS 0.007 0.001 HIS C 63 PHE 0.024 0.002 PHE A 374 TYR 0.016 0.002 TYR C 229 ARG 0.007 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 16) link_NAG-ASN : angle 3.64995 ( 48) link_ALPHA1-6 : bond 0.00325 ( 2) link_ALPHA1-6 : angle 1.58941 ( 6) link_BETA1-4 : bond 0.01000 ( 21) link_BETA1-4 : angle 3.34247 ( 63) link_ALPHA1-3 : bond 0.02272 ( 1) link_ALPHA1-3 : angle 2.21366 ( 3) hydrogen bonds : bond 0.03544 ( 184) hydrogen bonds : angle 6.92001 ( 483) link_BETA1-6 : bond 0.01064 ( 1) link_BETA1-6 : angle 2.01008 ( 3) SS BOND : bond 0.00277 ( 16) SS BOND : angle 1.33448 ( 32) covalent geometry : bond 0.00327 ( 9023) covalent geometry : angle 0.69860 (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 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.943 Fit side-chains REVERT: D 906 PRO cc_start: 0.6757 (Cg_endo) cc_final: 0.6553 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.5188 (pt) REVERT: D 1017 PHE cc_start: 0.6781 (m-80) cc_final: 0.6409 (m-80) REVERT: A 272 PHE cc_start: 0.4268 (OUTLIER) cc_final: 0.3799 (m-80) REVERT: A 316 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6659 (tm) REVERT: A 328 ASN cc_start: 0.3488 (OUTLIER) cc_final: 0.3139 (m-40) REVERT: A 357 VAL cc_start: 0.6146 (OUTLIER) cc_final: 0.5566 (m) outliers start: 32 outliers final: 19 residues processed: 126 average time/residue: 0.9069 time to fit residues: 126.8558 Evaluate side-chains 124 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 885 LYS Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain 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 357 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 467 VAL 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 691 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.251601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.225388 restraints weight = 13817.964| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 2.98 r_work: 0.4560 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9080 Z= 0.155 Angle : 0.764 12.943 12440 Z= 0.348 Chirality : 0.051 0.554 1458 Planarity : 0.005 0.072 1560 Dihedral : 9.961 69.913 1985 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.55 % Favored : 91.07 % Rotamer: Outliers : 3.16 % Allowed : 13.74 % Favored : 83.10 % 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: -1.54 (0.26), residues: 1064 helix: 0.30 (0.78), residues: 55 sheet: -0.89 (0.31), residues: 280 loop : -1.22 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 819 HIS 0.011 0.001 HIS C 63 PHE 0.046 0.002 PHE A 374 TYR 0.023 0.002 TYR A 324 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 16) link_NAG-ASN : angle 3.52596 ( 48) link_ALPHA1-6 : bond 0.00294 ( 2) link_ALPHA1-6 : angle 1.59502 ( 6) link_BETA1-4 : bond 0.00997 ( 21) link_BETA1-4 : angle 3.30031 ( 63) link_ALPHA1-3 : bond 0.02149 ( 1) link_ALPHA1-3 : angle 2.22581 ( 3) hydrogen bonds : bond 0.03472 ( 184) hydrogen bonds : angle 6.74227 ( 483) link_BETA1-6 : bond 0.00994 ( 1) link_BETA1-6 : angle 1.96532 ( 3) SS BOND : bond 0.00315 ( 16) SS BOND : angle 1.19408 ( 32) covalent geometry : bond 0.00336 ( 9023) covalent geometry : angle 0.69239 (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 126 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.977 Fit side-chains REVERT: C 23 LYS cc_start: 0.5192 (OUTLIER) cc_final: 0.4172 (pttt) REVERT: D 906 PRO cc_start: 0.6726 (Cg_endo) cc_final: 0.6511 (Cg_exo) REVERT: D 955 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5142 (pt) REVERT: D 1017 PHE cc_start: 0.6862 (m-80) cc_final: 0.6477 (m-80) REVERT: A 272 PHE cc_start: 0.4166 (OUTLIER) cc_final: 0.3729 (m-80) REVERT: A 316 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6622 (tm) REVERT: A 328 ASN cc_start: 0.3487 (OUTLIER) cc_final: 0.3191 (m-40) REVERT: A 357 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5589 (m) outliers start: 29 outliers final: 16 residues processed: 117 average time/residue: 0.7740 time to fit residues: 101.4418 Evaluate side-chains 118 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 447 MET 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 605 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.250193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.223980 restraints weight = 13693.104| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 2.96 r_work: 0.4553 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9080 Z= 0.156 Angle : 0.759 12.861 12440 Z= 0.346 Chirality : 0.051 0.553 1458 Planarity : 0.004 0.063 1560 Dihedral : 9.759 71.166 1985 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.74 % Favored : 90.88 % Rotamer: Outliers : 2.84 % Allowed : 14.39 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.57 (0.26), residues: 1064 helix: 0.23 (0.78), residues: 55 sheet: -0.72 (0.32), residues: 267 loop : -1.33 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 819 HIS 0.006 0.001 HIS C 63 PHE 0.029 0.002 PHE A 374 TYR 0.019 0.002 TYR C 175 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 16) link_NAG-ASN : angle 3.51253 ( 48) link_ALPHA1-6 : bond 0.00292 ( 2) link_ALPHA1-6 : angle 1.57672 ( 6) link_BETA1-4 : bond 0.00985 ( 21) link_BETA1-4 : angle 3.27647 ( 63) link_ALPHA1-3 : bond 0.02137 ( 1) link_ALPHA1-3 : angle 2.29011 ( 3) hydrogen bonds : bond 0.03497 ( 184) hydrogen bonds : angle 6.73778 ( 483) link_BETA1-6 : bond 0.00972 ( 1) link_BETA1-6 : angle 1.92554 ( 3) SS BOND : bond 0.00328 ( 16) SS BOND : angle 1.14944 ( 32) covalent geometry : bond 0.00331 ( 9023) covalent geometry : angle 0.68763 (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 122 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.912 Fit side-chains REVERT: C 23 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.4212 (pttt) REVERT: D 906 PRO cc_start: 0.6683 (Cg_endo) cc_final: 0.6461 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6908 (m-80) cc_final: 0.6504 (m-80) REVERT: A 272 PHE cc_start: 0.4172 (OUTLIER) cc_final: 0.3728 (m-80) REVERT: A 316 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6663 (tm) REVERT: A 328 ASN cc_start: 0.3449 (OUTLIER) cc_final: 0.3190 (m-40) outliers start: 26 outliers final: 18 residues processed: 114 average time/residue: 0.6914 time to fit residues: 88.7615 Evaluate side-chains 117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 467 VAL 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 605 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.250217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.224238 restraints weight = 13600.834| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 2.94 r_work: 0.4549 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9080 Z= 0.159 Angle : 0.759 12.824 12440 Z= 0.346 Chirality : 0.051 0.556 1458 Planarity : 0.005 0.074 1560 Dihedral : 9.622 70.424 1985 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.65 % Favored : 90.98 % Rotamer: Outliers : 2.62 % Allowed : 14.94 % Favored : 82.44 % 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: -1.60 (0.26), residues: 1064 helix: -0.00 (0.73), residues: 61 sheet: -0.83 (0.31), residues: 281 loop : -1.30 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 819 HIS 0.004 0.001 HIS D 844 PHE 0.021 0.002 PHE A 568 TYR 0.017 0.002 TYR A 507 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 16) link_NAG-ASN : angle 3.50120 ( 48) link_ALPHA1-6 : bond 0.00292 ( 2) link_ALPHA1-6 : angle 1.58455 ( 6) link_BETA1-4 : bond 0.00987 ( 21) link_BETA1-4 : angle 3.26614 ( 63) link_ALPHA1-3 : bond 0.02108 ( 1) link_ALPHA1-3 : angle 2.25616 ( 3) hydrogen bonds : bond 0.03504 ( 184) hydrogen bonds : angle 6.71592 ( 483) link_BETA1-6 : bond 0.00947 ( 1) link_BETA1-6 : angle 1.89247 ( 3) SS BOND : bond 0.00356 ( 16) SS BOND : angle 1.07191 ( 32) covalent geometry : bond 0.00337 ( 9023) covalent geometry : angle 0.68835 (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 123 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: C 23 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4179 (pttt) REVERT: D 906 PRO cc_start: 0.6704 (Cg_endo) cc_final: 0.6478 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6810 (m-80) cc_final: 0.6426 (m-80) REVERT: A 272 PHE cc_start: 0.4169 (OUTLIER) cc_final: 0.3726 (m-80) REVERT: A 316 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6685 (tm) REVERT: A 357 VAL cc_start: 0.6245 (OUTLIER) cc_final: 0.5662 (m) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.7673 time to fit residues: 99.2303 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 967 CYS Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 467 VAL 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 605 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.249486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.223403 restraints weight = 13476.778| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 2.97 r_work: 0.4542 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5579 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9080 Z= 0.172 Angle : 0.772 12.763 12440 Z= 0.356 Chirality : 0.052 0.552 1458 Planarity : 0.005 0.066 1560 Dihedral : 9.557 70.805 1985 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.02 % Favored : 90.60 % Rotamer: Outliers : 2.73 % Allowed : 15.05 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.63 (0.26), residues: 1064 helix: -0.05 (0.74), residues: 61 sheet: -0.82 (0.32), residues: 276 loop : -1.34 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 819 HIS 0.014 0.002 HIS C 63 PHE 0.063 0.002 PHE A 374 TYR 0.022 0.002 TYR D1004 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 16) link_NAG-ASN : angle 3.53520 ( 48) link_ALPHA1-6 : bond 0.00276 ( 2) link_ALPHA1-6 : angle 1.61919 ( 6) link_BETA1-4 : bond 0.00992 ( 21) link_BETA1-4 : angle 3.24638 ( 63) link_ALPHA1-3 : bond 0.02165 ( 1) link_ALPHA1-3 : angle 2.23317 ( 3) hydrogen bonds : bond 0.03633 ( 184) hydrogen bonds : angle 6.76464 ( 483) link_BETA1-6 : bond 0.00933 ( 1) link_BETA1-6 : angle 1.86397 ( 3) SS BOND : bond 0.00333 ( 16) SS BOND : angle 1.14809 ( 32) covalent geometry : bond 0.00364 ( 9023) covalent geometry : angle 0.70244 (12285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5990.64 seconds wall clock time: 104 minutes 3.06 seconds (6243.06 seconds total)