Starting phenix.real_space_refine on Wed Sep 17 13:03:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi4_60121/09_2025/8zi4_60121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi4_60121/09_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_60121/09_2025/8zi4_60121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi4_60121/09_2025/8zi4_60121.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi4_60121/09_2025/8zi4_60121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi4_60121/09_2025/8zi4_60121.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5518 2.51 5 N 1426 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8818 Number of models: 1 Model: "" Number of chains: 17 Chain: "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: 2.71, per 1000 atoms: 0.31 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: 1.14 Conformation dependent library (CDL) restraints added in 354.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 8.6% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 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: 1.81 Time building geometry restraints manager: 1.39 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- 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 : 9.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (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 ARG 0.001 0.000 ARG A 368 TYR 0.005 0.001 TYR A 546 PHE 0.007 0.001 PHE A 334 TRP 0.003 0.001 TRP A 366 HIS 0.001 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9023) covalent geometry : angle 0.75077 (12285) SS BOND : bond 0.00123 ( 16) SS BOND : angle 0.49932 ( 32) hydrogen bonds : bond 0.25220 ( 184) hydrogen bonds : angle 10.42144 ( 483) link_ALPHA1-3 : bond 0.00777 ( 1) link_ALPHA1-3 : angle 1.47110 ( 3) link_ALPHA1-6 : bond 0.00342 ( 2) link_ALPHA1-6 : angle 1.67782 ( 6) link_BETA1-4 : bond 0.00937 ( 21) link_BETA1-4 : angle 3.63939 ( 63) link_BETA1-6 : bond 0.00683 ( 1) link_BETA1-6 : angle 1.27728 ( 3) link_NAG-ASN : bond 0.01169 ( 16) link_NAG-ASN : angle 5.34567 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.253 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: 0.3997 time to fit residues: 59.9470 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 : 0.307 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN C 222 GLN D 844 HIS D 881 HIS D 921 GLN D 929 GLN A 310 GLN A 348 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 466 GLN A 619 ASN A 647 HIS A 700 HIS A 768 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.252892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.226530 restraints weight = 13750.127| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 2.96 r_work: 0.4568 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9080 Z= 0.266 Angle : 0.948 13.289 12440 Z= 0.431 Chirality : 0.057 0.599 1458 Planarity : 0.005 0.051 1560 Dihedral : 16.563 89.855 1998 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % Rotamer: Outliers : 3.05 % Allowed : 8.62 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.26), residues: 1064 helix: 0.09 (0.72), residues: 60 sheet: 0.09 (0.32), residues: 272 loop : -0.90 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 403 TYR 0.024 0.002 TYR D 868 PHE 0.032 0.003 PHE A 568 TRP 0.020 0.003 TRP C 144 HIS 0.009 0.002 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9023) covalent geometry : angle 0.87066 (12285) SS BOND : bond 0.01321 ( 16) SS BOND : angle 1.41178 ( 32) hydrogen bonds : bond 0.05408 ( 184) hydrogen bonds : angle 7.24405 ( 483) link_ALPHA1-3 : bond 0.01627 ( 1) link_ALPHA1-3 : angle 2.48037 ( 3) link_ALPHA1-6 : bond 0.00424 ( 2) link_ALPHA1-6 : angle 2.28063 ( 6) link_BETA1-4 : bond 0.01030 ( 21) link_BETA1-4 : angle 3.93773 ( 63) link_BETA1-6 : bond 0.00940 ( 1) link_BETA1-6 : angle 2.25851 ( 3) link_NAG-ASN : bond 0.00941 ( 16) link_NAG-ASN : angle 3.98956 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6752 (Cg_endo) cc_final: 0.6512 (Cg_exo) REVERT: D 954 MET cc_start: 0.6584 (mtm) cc_final: 0.6317 (mtm) REVERT: A 272 PHE cc_start: 0.4030 (OUTLIER) cc_final: 0.3745 (m-80) REVERT: A 277 THR cc_start: 0.7693 (p) cc_final: 0.7326 (t) REVERT: A 328 ASN cc_start: 0.3520 (OUTLIER) cc_final: 0.2815 (m-40) REVERT: A 682 ASN cc_start: 0.2101 (OUTLIER) cc_final: 0.1608 (p0) outliers start: 28 outliers final: 12 residues processed: 135 average time/residue: 0.3938 time to fit residues: 58.5232 Evaluate side-chains 126 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 849 LEU 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 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 552 CYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL 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 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 39 optimal weight: 0.0070 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.252917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.226448 restraints weight = 13698.104| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 2.93 r_work: 0.4567 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9080 Z= 0.185 Angle : 0.809 13.788 12440 Z= 0.360 Chirality : 0.054 0.559 1458 Planarity : 0.005 0.051 1560 Dihedral : 13.667 81.617 1992 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.77 % Favored : 92.86 % Rotamer: Outliers : 2.51 % Allowed : 10.58 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.26), residues: 1064 helix: 0.23 (0.73), residues: 60 sheet: -0.10 (0.31), residues: 275 loop : -1.00 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.016 0.002 TYR D 948 PHE 0.017 0.002 PHE A 568 TRP 0.033 0.002 TRP D 819 HIS 0.006 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9023) covalent geometry : angle 0.73246 (12285) SS BOND : bond 0.00359 ( 16) SS BOND : angle 0.87667 ( 32) hydrogen bonds : bond 0.04370 ( 184) hydrogen bonds : angle 6.95126 ( 483) link_ALPHA1-3 : bond 0.01908 ( 1) link_ALPHA1-3 : angle 2.38692 ( 3) link_ALPHA1-6 : bond 0.00239 ( 2) link_ALPHA1-6 : angle 1.86249 ( 6) link_BETA1-4 : bond 0.01025 ( 21) link_BETA1-4 : angle 3.59169 ( 63) link_BETA1-6 : bond 0.00931 ( 1) link_BETA1-6 : angle 1.98091 ( 3) link_NAG-ASN : bond 0.00627 ( 16) link_NAG-ASN : angle 3.71064 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6786 (Cg_endo) cc_final: 0.6554 (Cg_exo) REVERT: D 954 MET cc_start: 0.6492 (mtm) cc_final: 0.6286 (mtt) REVERT: D 1017 PHE cc_start: 0.6544 (m-80) cc_final: 0.6210 (m-80) REVERT: A 272 PHE cc_start: 0.4273 (OUTLIER) cc_final: 0.3659 (m-80) REVERT: A 277 THR cc_start: 0.7664 (p) cc_final: 0.7319 (t) REVERT: A 328 ASN cc_start: 0.3817 (OUTLIER) cc_final: 0.3312 (m110) REVERT: A 528 PHE cc_start: 0.5015 (OUTLIER) cc_final: 0.4791 (m-10) outliers start: 23 outliers final: 14 residues processed: 120 average time/residue: 0.4088 time to fit residues: 53.8974 Evaluate side-chains 117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 871 ARG Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 528 PHE 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 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.252867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.226280 restraints weight = 13878.478| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 2.92 r_work: 0.4567 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9080 Z= 0.162 Angle : 0.762 13.722 12440 Z= 0.340 Chirality : 0.052 0.576 1458 Planarity : 0.004 0.054 1560 Dihedral : 11.537 73.012 1989 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.18 % Favored : 91.45 % Rotamer: Outliers : 3.49 % Allowed : 10.58 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.26), residues: 1064 helix: 0.14 (0.74), residues: 60 sheet: -0.27 (0.31), residues: 282 loop : -1.08 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.021 0.002 TYR C 175 PHE 0.031 0.002 PHE A 568 TRP 0.029 0.002 TRP D 819 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9023) covalent geometry : angle 0.68611 (12285) SS BOND : bond 0.00326 ( 16) SS BOND : angle 0.89814 ( 32) hydrogen bonds : bond 0.03625 ( 184) hydrogen bonds : angle 6.72724 ( 483) link_ALPHA1-3 : bond 0.02451 ( 1) link_ALPHA1-3 : angle 2.42795 ( 3) link_ALPHA1-6 : bond 0.00223 ( 2) link_ALPHA1-6 : angle 1.89013 ( 6) link_BETA1-4 : bond 0.01022 ( 21) link_BETA1-4 : angle 3.49498 ( 63) link_BETA1-6 : bond 0.00997 ( 1) link_BETA1-6 : angle 1.98470 ( 3) link_NAG-ASN : bond 0.00593 ( 16) link_NAG-ASN : angle 3.49401 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6741 (Cg_endo) cc_final: 0.6514 (Cg_exo) REVERT: D 976 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5123 (mtt) REVERT: D 1017 PHE cc_start: 0.6664 (m-80) cc_final: 0.6296 (m-80) REVERT: A 272 PHE cc_start: 0.4253 (OUTLIER) cc_final: 0.3651 (m-80) REVERT: A 277 THR cc_start: 0.7573 (p) cc_final: 0.7232 (t) REVERT: A 316 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6670 (tm) REVERT: A 328 ASN cc_start: 0.3667 (OUTLIER) cc_final: 0.3346 (m110) REVERT: A 578 ASP cc_start: 0.6826 (m-30) cc_final: 0.6555 (m-30) outliers start: 32 outliers final: 18 residues processed: 124 average time/residue: 0.3984 time to fit residues: 54.6999 Evaluate side-chains 124 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 TYR 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 933 VAL Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 725 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.251731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.225749 restraints weight = 13957.175| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 2.98 r_work: 0.4562 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9080 Z= 0.156 Angle : 0.740 13.469 12440 Z= 0.333 Chirality : 0.051 0.561 1458 Planarity : 0.004 0.053 1560 Dihedral : 10.834 71.816 1989 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.42 % Favored : 92.20 % Rotamer: Outliers : 4.14 % Allowed : 10.69 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.26), residues: 1064 helix: 0.59 (0.79), residues: 54 sheet: -0.35 (0.31), residues: 270 loop : -1.12 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.015 0.001 TYR C 175 PHE 0.046 0.002 PHE A 374 TRP 0.030 0.002 TRP D 819 HIS 0.005 0.001 HIS D 881 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9023) covalent geometry : angle 0.66654 (12285) SS BOND : bond 0.00348 ( 16) SS BOND : angle 0.81031 ( 32) hydrogen bonds : bond 0.03536 ( 184) hydrogen bonds : angle 6.63029 ( 483) link_ALPHA1-3 : bond 0.02377 ( 1) link_ALPHA1-3 : angle 2.40766 ( 3) link_ALPHA1-6 : bond 0.00268 ( 2) link_ALPHA1-6 : angle 1.71081 ( 6) link_BETA1-4 : bond 0.00998 ( 21) link_BETA1-4 : angle 3.37594 ( 63) link_BETA1-6 : bond 0.00988 ( 1) link_BETA1-6 : angle 1.93903 ( 3) link_NAG-ASN : bond 0.00581 ( 16) link_NAG-ASN : angle 3.46838 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 906 PRO cc_start: 0.6777 (Cg_endo) cc_final: 0.6541 (Cg_exo) REVERT: D 976 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.5081 (mtt) REVERT: D 1017 PHE cc_start: 0.6675 (m-80) cc_final: 0.6348 (m-80) REVERT: A 272 PHE cc_start: 0.4235 (OUTLIER) cc_final: 0.3621 (m-80) REVERT: A 316 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6758 (tm) REVERT: A 328 ASN cc_start: 0.3676 (OUTLIER) cc_final: 0.3231 (m-40) outliers start: 38 outliers final: 18 residues processed: 134 average time/residue: 0.3752 time to fit residues: 55.8682 Evaluate side-chains 126 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 TYR 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 933 VAL Chi-restraints excluded: chain D residue 976 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 342 TYR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 725 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN 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 = 0.251464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.225393 restraints weight = 13674.108| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 2.90 r_work: 0.4565 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9080 Z= 0.187 Angle : 0.777 13.416 12440 Z= 0.355 Chirality : 0.052 0.570 1458 Planarity : 0.005 0.058 1560 Dihedral : 10.631 68.868 1989 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.74 % Favored : 90.88 % Rotamer: Outliers : 4.36 % Allowed : 11.45 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.26), residues: 1064 helix: 0.38 (0.79), residues: 55 sheet: -0.43 (0.31), residues: 275 loop : -1.18 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 611 TYR 0.016 0.002 TYR C 175 PHE 0.042 0.002 PHE A 374 TRP 0.035 0.002 TRP D 819 HIS 0.005 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9023) covalent geometry : angle 0.69882 (12285) SS BOND : bond 0.00448 ( 16) SS BOND : angle 1.47709 ( 32) hydrogen bonds : bond 0.03732 ( 184) hydrogen bonds : angle 6.83021 ( 483) link_ALPHA1-3 : bond 0.02401 ( 1) link_ALPHA1-3 : angle 2.33438 ( 3) link_ALPHA1-6 : bond 0.00191 ( 2) link_ALPHA1-6 : angle 1.70723 ( 6) link_BETA1-4 : bond 0.00980 ( 21) link_BETA1-4 : angle 3.35431 ( 63) link_BETA1-6 : bond 0.00932 ( 1) link_BETA1-6 : angle 1.93317 ( 3) link_NAG-ASN : bond 0.00604 ( 16) link_NAG-ASN : angle 3.77534 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: C 23 LYS cc_start: 0.5317 (OUTLIER) cc_final: 0.4372 (pttt) REVERT: D 906 PRO cc_start: 0.6746 (Cg_endo) cc_final: 0.6518 (Cg_exo) REVERT: D 976 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.5492 (mtt) REVERT: D 1017 PHE cc_start: 0.6726 (m-80) cc_final: 0.6374 (m-80) REVERT: A 272 PHE cc_start: 0.4252 (OUTLIER) cc_final: 0.3659 (m-80) REVERT: A 277 THR cc_start: 0.7502 (p) cc_final: 0.7154 (t) REVERT: A 316 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6744 (tm) REVERT: A 328 ASN cc_start: 0.3674 (OUTLIER) cc_final: 0.3220 (m-40) REVERT: A 350 GLU cc_start: 0.7201 (pm20) cc_final: 0.6934 (pm20) outliers start: 40 outliers final: 23 residues processed: 128 average time/residue: 0.3936 time to fit residues: 55.8554 Evaluate side-chains 129 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 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 936 LEU Chi-restraints excluded: chain D residue 945 MET 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 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 725 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.0050 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.253743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.227931 restraints weight = 13779.192| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 2.93 r_work: 0.4583 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9080 Z= 0.123 Angle : 0.722 12.913 12440 Z= 0.325 Chirality : 0.050 0.549 1458 Planarity : 0.004 0.054 1560 Dihedral : 10.000 70.701 1985 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.95 % Favored : 92.67 % Rotamer: Outliers : 3.27 % Allowed : 12.54 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.26), residues: 1064 helix: 0.55 (0.79), residues: 54 sheet: -0.47 (0.32), residues: 266 loop : -1.05 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.017 0.001 TYR C 175 PHE 0.035 0.002 PHE A 374 TRP 0.033 0.002 TRP D 819 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9023) covalent geometry : angle 0.64715 (12285) SS BOND : bond 0.00337 ( 16) SS BOND : angle 1.17942 ( 32) hydrogen bonds : bond 0.03147 ( 184) hydrogen bonds : angle 6.55555 ( 483) link_ALPHA1-3 : bond 0.02292 ( 1) link_ALPHA1-3 : angle 2.42370 ( 3) link_ALPHA1-6 : bond 0.00326 ( 2) link_ALPHA1-6 : angle 1.51141 ( 6) link_BETA1-4 : bond 0.00995 ( 21) link_BETA1-4 : angle 3.25046 ( 63) link_BETA1-6 : bond 0.01070 ( 1) link_BETA1-6 : angle 1.97113 ( 3) link_NAG-ASN : bond 0.00565 ( 16) link_NAG-ASN : angle 3.48404 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: C 23 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4310 (pttt) REVERT: D 906 PRO cc_start: 0.6638 (Cg_endo) cc_final: 0.6432 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6768 (m-80) cc_final: 0.6436 (m-80) REVERT: A 272 PHE cc_start: 0.4090 (OUTLIER) cc_final: 0.3545 (m-80) REVERT: A 316 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6679 (tm) REVERT: A 328 ASN cc_start: 0.3621 (OUTLIER) cc_final: 0.3159 (m-40) outliers start: 30 outliers final: 16 residues processed: 121 average time/residue: 0.3637 time to fit residues: 49.2545 Evaluate side-chains 120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 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 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 725 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.252168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.226333 restraints weight = 13607.257| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 2.90 r_work: 0.4569 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.3821 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= 0.142 Angle : 0.733 12.892 12440 Z= 0.330 Chirality : 0.050 0.553 1458 Planarity : 0.005 0.097 1560 Dihedral : 9.799 69.470 1985 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % Rotamer: Outliers : 3.60 % Allowed : 12.76 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.26), residues: 1064 helix: 0.53 (0.80), residues: 54 sheet: -0.45 (0.32), residues: 264 loop : -1.10 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 611 TYR 0.037 0.002 TYR A 427 PHE 0.039 0.002 PHE A 374 TRP 0.039 0.002 TRP D 819 HIS 0.006 0.001 HIS D 881 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9023) covalent geometry : angle 0.66160 (12285) SS BOND : bond 0.00305 ( 16) SS BOND : angle 1.09273 ( 32) hydrogen bonds : bond 0.03327 ( 184) hydrogen bonds : angle 6.41755 ( 483) link_ALPHA1-3 : bond 0.02158 ( 1) link_ALPHA1-3 : angle 2.38600 ( 3) link_ALPHA1-6 : bond 0.00314 ( 2) link_ALPHA1-6 : angle 1.57126 ( 6) link_BETA1-4 : bond 0.00983 ( 21) link_BETA1-4 : angle 3.23165 ( 63) link_BETA1-6 : bond 0.00968 ( 1) link_BETA1-6 : angle 1.91355 ( 3) link_NAG-ASN : bond 0.00562 ( 16) link_NAG-ASN : angle 3.45753 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 23 LYS cc_start: 0.5344 (OUTLIER) cc_final: 0.4401 (pttt) REVERT: D 906 PRO cc_start: 0.6642 (Cg_endo) cc_final: 0.6422 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6814 (m-80) cc_final: 0.6462 (m-80) REVERT: A 272 PHE cc_start: 0.4141 (OUTLIER) cc_final: 0.3647 (m-80) REVERT: A 277 THR cc_start: 0.7418 (p) cc_final: 0.7079 (t) REVERT: A 316 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6712 (tm) REVERT: A 578 ASP cc_start: 0.6912 (m-30) cc_final: 0.6704 (m-30) outliers start: 33 outliers final: 21 residues processed: 120 average time/residue: 0.3884 time to fit residues: 51.7795 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 : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain D residue 815 VAL 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 1007 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 725 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN ** 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 = 0.4879 r_free = 0.4879 target = 0.248181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.221992 restraints weight = 13474.552| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 2.93 r_work: 0.4538 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9080 Z= 0.222 Angle : 0.815 12.884 12440 Z= 0.375 Chirality : 0.053 0.558 1458 Planarity : 0.005 0.095 1560 Dihedral : 10.132 69.874 1983 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.21 % Favored : 90.41 % Rotamer: Outliers : 3.49 % Allowed : 13.09 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.26), residues: 1064 helix: 0.19 (0.79), residues: 55 sheet: -0.79 (0.31), residues: 286 loop : -1.28 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 611 TYR 0.048 0.002 TYR A 427 PHE 0.044 0.003 PHE A 374 TRP 0.051 0.003 TRP D 819 HIS 0.007 0.002 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9023) covalent geometry : angle 0.74723 (12285) SS BOND : bond 0.00416 ( 16) SS BOND : angle 1.25058 ( 32) hydrogen bonds : bond 0.04024 ( 184) hydrogen bonds : angle 6.70153 ( 483) link_ALPHA1-3 : bond 0.02133 ( 1) link_ALPHA1-3 : angle 2.17728 ( 3) link_ALPHA1-6 : bond 0.00201 ( 2) link_ALPHA1-6 : angle 1.70599 ( 6) link_BETA1-4 : bond 0.00973 ( 21) link_BETA1-4 : angle 3.29281 ( 63) link_BETA1-6 : bond 0.00848 ( 1) link_BETA1-6 : angle 1.84458 ( 3) link_NAG-ASN : bond 0.00687 ( 16) link_NAG-ASN : angle 3.59734 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.321 Fit side-chains REVERT: C 23 LYS cc_start: 0.5525 (OUTLIER) cc_final: 0.4483 (pttt) REVERT: D 906 PRO cc_start: 0.6776 (Cg_endo) cc_final: 0.6551 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6810 (m-80) cc_final: 0.6433 (m-80) REVERT: A 272 PHE cc_start: 0.4080 (OUTLIER) cc_final: 0.3468 (m-80) REVERT: A 316 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6728 (tm) REVERT: A 578 ASP cc_start: 0.7044 (m-30) cc_final: 0.6824 (m-30) REVERT: A 632 THR cc_start: 0.5697 (m) cc_final: 0.5458 (p) outliers start: 32 outliers final: 18 residues processed: 123 average time/residue: 0.4019 time to fit residues: 54.5228 Evaluate side-chains 121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 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 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 334 PHE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 574 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 865 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.250499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.224115 restraints weight = 13601.003| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 3.00 r_work: 0.4545 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9080 Z= 0.154 Angle : 0.772 12.801 12440 Z= 0.351 Chirality : 0.052 0.551 1458 Planarity : 0.005 0.088 1560 Dihedral : 9.766 71.722 1983 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.46 % Favored : 91.17 % Rotamer: Outliers : 2.94 % Allowed : 14.39 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.26), residues: 1064 helix: 0.25 (0.78), residues: 55 sheet: -0.55 (0.32), residues: 255 loop : -1.30 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 611 TYR 0.043 0.002 TYR A 427 PHE 0.040 0.002 PHE A 374 TRP 0.050 0.002 TRP D 819 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9023) covalent geometry : angle 0.69305 (12285) SS BOND : bond 0.00322 ( 16) SS BOND : angle 1.04050 ( 32) hydrogen bonds : bond 0.03470 ( 184) hydrogen bonds : angle 6.62193 ( 483) link_ALPHA1-3 : bond 0.02114 ( 1) link_ALPHA1-3 : angle 2.17791 ( 3) link_ALPHA1-6 : bond 0.00344 ( 2) link_ALPHA1-6 : angle 1.57318 ( 6) link_BETA1-4 : bond 0.00979 ( 21) link_BETA1-4 : angle 3.23867 ( 63) link_BETA1-6 : bond 0.00966 ( 1) link_BETA1-6 : angle 1.88235 ( 3) link_NAG-ASN : bond 0.00577 ( 16) link_NAG-ASN : angle 4.04177 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.313 Fit side-chains REVERT: C 23 LYS cc_start: 0.5487 (OUTLIER) cc_final: 0.4505 (pttt) REVERT: D 906 PRO cc_start: 0.6739 (Cg_endo) cc_final: 0.6519 (Cg_exo) REVERT: D 1017 PHE cc_start: 0.6814 (m-80) cc_final: 0.6427 (m-80) REVERT: A 272 PHE cc_start: 0.3934 (OUTLIER) cc_final: 0.3301 (m-80) REVERT: A 307 PHE cc_start: 0.6791 (m-80) cc_final: 0.5758 (m-80) REVERT: A 316 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6667 (tm) REVERT: A 578 ASP cc_start: 0.6990 (m-30) cc_final: 0.6771 (m-30) REVERT: A 632 THR cc_start: 0.5723 (m) cc_final: 0.5485 (p) outliers start: 27 outliers final: 17 residues processed: 116 average time/residue: 0.4022 time to fit residues: 51.4134 Evaluate side-chains 118 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain D residue 827 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 865 ASN Chi-restraints excluded: chain D residue 893 GLN Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 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 334 PHE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 574 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 85 optimal weight: 0.0570 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 865 ASN D 869 ASN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN A 660 ASN A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.250665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.224760 restraints weight = 13519.204| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 2.94 r_work: 0.4551 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9080 Z= 0.151 Angle : 0.774 12.849 12440 Z= 0.352 Chirality : 0.052 0.553 1458 Planarity : 0.005 0.085 1560 Dihedral : 9.586 71.006 1983 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.49 % Favored : 90.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.26), residues: 1064 helix: 0.26 (0.77), residues: 55 sheet: -0.65 (0.32), residues: 262 loop : -1.31 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 611 TYR 0.038 0.002 TYR A 427 PHE 0.029 0.002 PHE A 452 TRP 0.052 0.002 TRP D 819 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9023) covalent geometry : angle 0.69699 (12285) SS BOND : bond 0.00298 ( 16) SS BOND : angle 1.53652 ( 32) hydrogen bonds : bond 0.03374 ( 184) hydrogen bonds : angle 6.56367 ( 483) link_ALPHA1-3 : bond 0.02065 ( 1) link_ALPHA1-3 : angle 2.21524 ( 3) link_ALPHA1-6 : bond 0.00250 ( 2) link_ALPHA1-6 : angle 1.57366 ( 6) link_BETA1-4 : bond 0.00977 ( 21) link_BETA1-4 : angle 3.20130 ( 63) link_BETA1-6 : bond 0.00967 ( 1) link_BETA1-6 : angle 1.87971 ( 3) link_NAG-ASN : bond 0.00571 ( 16) link_NAG-ASN : angle 3.86560 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3096.86 seconds wall clock time: 53 minutes 46.03 seconds (3226.03 seconds total)