Starting phenix.real_space_refine on Sat Aug 23 00:29:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ziy_60133/08_2025/8ziy_60133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ziy_60133/08_2025/8ziy_60133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ziy_60133/08_2025/8ziy_60133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ziy_60133/08_2025/8ziy_60133.map" model { file = "/net/cci-nas-00/data/ceres_data/8ziy_60133/08_2025/8ziy_60133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ziy_60133/08_2025/8ziy_60133.cif" } resolution = 2.64 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= 0.002 sd= 0.028 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 5506 2.51 5 N 1424 2.21 5 O 1811 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8797 Number of models: 1 Model: "" Number of chains: 16 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: 4689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4689 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: 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: "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: 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: "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: 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: "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: 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: "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: 2.31, per 1000 atoms: 0.26 Number of scatterers: 8797 At special positions: 0 Unit cell: (85.744, 108.112, 154.712, 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 1811 8.00 N 1424 7.00 C 5506 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=4, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 801 " - " ASN A 503 " " NAG A 802 " - " ASN A 328 " " NAG A 803 " - " ASN A 682 " " 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 440 " " NAG I 1 " - " ASN A 335 " " NAG J 1 " - " ASN A 388 " " NAG K 1 " - " ASN A 470 " " NAG L 1 " - " ASN A 534 " " NAG M 1 " - " ASN A 630 " " NAG N 1 " - " ASN A 725 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 331.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 7.6% alpha, 23.2% 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 removed outlier: 3.938A pdb=" N TYR C 65 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.813A pdb=" N TYR C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.645A pdb=" N GLN D 942 " --> pdb=" O ASN D 938 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 1007 through 1009 No H-bonds generated for 'chain 'D' and resid 1007 through 1009' Processing helix chain 'D' and resid 1010 through 1015 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: 3.642A pdb=" N GLU A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.506A pdb=" N ILE A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 708 through 720 Processing sheet with id=AA1, first strand: chain 'C' and resid 39 through 42 removed outlier: 3.988A pdb=" N CYS C 48 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.613A 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 163 removed outlier: 7.124A pdb=" N VAL C 204 " --> pdb=" O GLN C 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AA4, first strand: chain 'D' and resid 789 through 790 removed outlier: 3.981A pdb=" N CYS D 956 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU D 985 " --> pdb=" O CYS D 977 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS D 977 " --> pdb=" O LEU D 985 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 913 " --> pdb=" O PRO D 974 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 855 through 858 removed outlier: 3.523A pdb=" N VAL D 855 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 841 " --> pdb=" O VAL D 855 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR D 804 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY D 811 " --> pdb=" O ALA D 823 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA D 823 " --> pdb=" O GLY D 811 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 861 " --> pdb=" O HIS D 881 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 190 Processing sheet with id=AA7, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA8, first strand: chain 'A' and resid 235 through 239 removed outlier: 3.864A pdb=" N GLY A 236 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.090A pdb=" N LYS A 436 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE A 452 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE A 441 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR A 450 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.588A pdb=" N GLU A 367 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 395 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 12.573A pdb=" N PHE A 392 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP A 494 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 394 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 495 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 424 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 497 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS A 422 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 556 through 557 removed outlier: 6.450A pdb=" N VAL A 580 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 595 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 582 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB4, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.867A pdb=" N LYS A 628 " --> pdb=" O GLN A 569 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE A 571 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY A 626 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AB6, first strand: chain 'A' and resid 679 through 681 Processing sheet with id=AB7, first strand: chain 'A' and resid 728 through 729 removed outlier: 4.098A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 740 through 742 194 hydrogen bonds defined for protein. 495 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: 1.61 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1459 1.32 - 1.44: 2527 1.44 - 1.57: 4948 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 9002 Sorted by residual: bond pdb=" C GLN D 978 " pdb=" O GLN D 978 " ideal model delta sigma weight residual 1.233 1.195 0.039 1.28e-02 6.10e+03 9.10e+00 bond pdb=" C4 NAG G 2 " pdb=" O4 NAG G 2 " ideal model delta sigma weight residual 1.409 1.460 -0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" N ASN D 980 " pdb=" CA ASN D 980 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.03e+00 bond pdb=" C5 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.418 1.459 -0.041 2.00e-02 2.50e+03 4.29e+00 ... (remaining 8997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11895 1.87 - 3.73: 260 3.73 - 5.60: 75 5.60 - 7.47: 24 7.47 - 9.34: 3 Bond angle restraints: 12257 Sorted by residual: angle pdb=" C GLN C 197 " pdb=" CA GLN C 197 " pdb=" CB GLN C 197 " ideal model delta sigma weight residual 116.34 110.27 6.07 1.40e+00 5.10e-01 1.88e+01 angle pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" O3 NAG G 1 " ideal model delta sigma weight residual 108.05 117.39 -9.34 3.00e+00 1.11e-01 9.68e+00 angle pdb=" C5 NAG G 2 " pdb=" C4 NAG G 2 " pdb=" O4 NAG G 2 " ideal model delta sigma weight residual 111.70 120.90 -9.20 3.00e+00 1.11e-01 9.40e+00 angle pdb=" CA GLN D 978 " pdb=" C GLN D 978 " pdb=" O GLN D 978 " ideal model delta sigma weight residual 121.72 118.24 3.48 1.18e+00 7.18e-01 8.71e+00 angle pdb=" CA GLU D 979 " pdb=" C GLU D 979 " pdb=" O GLU D 979 " ideal model delta sigma weight residual 121.20 118.23 2.97 1.04e+00 9.25e-01 8.18e+00 ... (remaining 12252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 5603 23.94 - 47.88: 111 47.88 - 71.82: 55 71.82 - 95.75: 54 95.75 - 119.69: 37 Dihedral angle restraints: 5860 sinusoidal: 2803 harmonic: 3057 Sorted by residual: dihedral pdb=" C2 MAN K 4 " pdb=" C1 MAN K 4 " pdb=" O5 MAN K 4 " pdb=" C5 MAN K 4 " ideal model delta sinusoidal sigma weight residual -57.62 62.07 -119.69 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 288.71 176.59 112.12 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C3 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 47.62 -62.69 110.31 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 5857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1290 0.088 - 0.175: 147 0.175 - 0.262: 5 0.262 - 0.350: 9 0.350 - 0.437: 2 Chirality restraints: 1453 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 -2.16 -0.24 2.00e-02 2.50e+03 1.44e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.54e+01 chirality pdb=" C4 NAG G 2 " pdb=" C3 NAG G 2 " pdb=" C5 NAG G 2 " pdb=" O4 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.09 -0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 1450 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.376 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C7 NAG G 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.557 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 980 " 0.248 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" CG ASN D 980 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN D 980 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN D 980 " -0.450 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.168 2.00e-02 2.50e+03 1.35e-01 2.29e+02 pdb=" C7 NAG G 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.213 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.032 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 96 2.58 - 3.16: 7072 3.16 - 3.74: 13299 3.74 - 4.32: 18151 4.32 - 4.90: 29806 Nonbonded interactions: 68424 Sorted by model distance: nonbonded pdb=" OE2 GLU A 586 " pdb=" CG2 THR A 609 " model vdw 1.996 3.460 nonbonded pdb=" O3 NAG G 2 " pdb=" O7 NAG G 2 " model vdw 2.053 3.040 nonbonded pdb=" O3 NAG G 2 " pdb=" O2 BMA G 3 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR D 828 " pdb=" OE2 GLU A 581 " model vdw 2.202 3.040 nonbonded pdb=" OG SER C 195 " pdb=" O CYS C 220 " model vdw 2.206 3.040 ... (remaining 68419 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 'G' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.910 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 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 : 0.005 0.227 9062 Z= 0.241 Angle : 0.797 22.422 12409 Z= 0.326 Chirality : 0.055 0.437 1453 Planarity : 0.009 0.317 1557 Dihedral : 17.407 119.694 3860 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.77 % Favored : 92.86 % Rotamer: Outliers : 1.64 % Allowed : 3.60 % Favored : 94.76 % 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: -0.28 (0.27), residues: 1064 helix: 0.70 (0.68), residues: 64 sheet: 1.06 (0.33), residues: 263 loop : -0.78 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 872 TYR 0.008 0.001 TYR A 276 PHE 0.007 0.001 PHE A 392 TRP 0.006 0.000 TRP A 531 HIS 0.001 0.000 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9002) covalent geometry : angle 0.70781 (12257) SS BOND : bond 0.00122 ( 16) SS BOND : angle 0.49319 ( 32) hydrogen bonds : bond 0.24908 ( 194) hydrogen bonds : angle 10.02150 ( 495) Misc. bond : bond 0.00076 ( 4) link_ALPHA1-3 : bond 0.00337 ( 3) link_ALPHA1-3 : angle 1.72733 ( 9) link_ALPHA1-6 : bond 0.00419 ( 2) link_ALPHA1-6 : angle 1.59171 ( 6) link_BETA1-4 : bond 0.01049 ( 18) link_BETA1-4 : angle 3.47326 ( 54) link_BETA1-6 : bond 0.00444 ( 2) link_BETA1-6 : angle 0.85252 ( 6) link_NAG-ASN : bond 0.05853 ( 15) link_NAG-ASN : angle 4.78010 ( 45) *********************** 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 183 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.4928 (OUTLIER) cc_final: 0.4511 (pt) REVERT: A 493 ASP cc_start: 0.3397 (t0) cc_final: 0.3172 (t0) REVERT: A 633 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5512 (t) REVERT: A 660 ASN cc_start: 0.5595 (OUTLIER) cc_final: 0.5119 (m110) REVERT: A 707 TRP cc_start: 0.6009 (t-100) cc_final: 0.5596 (m100) outliers start: 15 outliers final: 4 residues processed: 180 average time/residue: 0.3882 time to fit residues: 76.9431 Evaluate side-chains 145 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 772 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN C 56 GLN C 63 HIS C 70 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN C 246 ASN D 875 ASN D 881 HIS D 902 GLN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 ASN A 300 ASN A 346 ASN A 435 HIS A 569 GLN A 769 HIS A 779 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.232426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.215196 restraints weight = 17794.738| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 3.42 r_work: 0.4717 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9062 Z= 0.179 Angle : 0.869 13.698 12409 Z= 0.383 Chirality : 0.056 0.477 1453 Planarity : 0.005 0.060 1557 Dihedral : 16.277 112.392 1963 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.42 % Favored : 92.20 % Rotamer: Outliers : 3.06 % Allowed : 10.26 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.26), residues: 1064 helix: -0.12 (0.67), residues: 61 sheet: 0.33 (0.30), residues: 290 loop : -1.09 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 830 TYR 0.038 0.002 TYR A 342 PHE 0.029 0.002 PHE A 392 TRP 0.023 0.002 TRP C 216 HIS 0.006 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9002) covalent geometry : angle 0.82183 (12257) SS BOND : bond 0.00284 ( 16) SS BOND : angle 1.06850 ( 32) hydrogen bonds : bond 0.04821 ( 194) hydrogen bonds : angle 7.28001 ( 495) Misc. bond : bond 0.00254 ( 4) link_ALPHA1-3 : bond 0.00617 ( 3) link_ALPHA1-3 : angle 2.57999 ( 9) link_ALPHA1-6 : bond 0.00624 ( 2) link_ALPHA1-6 : angle 2.65555 ( 6) link_BETA1-4 : bond 0.00978 ( 18) link_BETA1-4 : angle 3.29281 ( 54) link_BETA1-6 : bond 0.00244 ( 2) link_BETA1-6 : angle 1.24684 ( 6) link_NAG-ASN : bond 0.00525 ( 15) link_NAG-ASN : angle 2.80701 ( 45) *********************** 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 187 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.7262 (tp-100) cc_final: 0.7043 (tp-100) REVERT: C 182 ASN cc_start: 0.5177 (m-40) cc_final: 0.4257 (t0) REVERT: A 317 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.4843 (pt) REVERT: A 546 TYR cc_start: 0.4107 (m-80) cc_final: 0.3840 (m-80) REVERT: A 605 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7199 (p) outliers start: 28 outliers final: 9 residues processed: 168 average time/residue: 0.3945 time to fit residues: 72.9076 Evaluate side-chains 154 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 826 CYS Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 605 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN A 370 GLN A 453 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.223443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.205951 restraints weight = 17398.350| |-----------------------------------------------------------------------------| r_work (start): 0.4726 rms_B_bonded: 3.36 r_work: 0.4634 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 9062 Z= 0.301 Angle : 1.051 15.655 12409 Z= 0.477 Chirality : 0.063 0.411 1453 Planarity : 0.006 0.067 1557 Dihedral : 14.360 107.458 1957 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.30 % Favored : 90.23 % Rotamer: Outliers : 3.60 % Allowed : 10.37 % Favored : 86.03 % 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: -1.81 (0.24), residues: 1064 helix: -1.22 (0.56), residues: 61 sheet: -0.44 (0.29), residues: 274 loop : -1.59 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 870 TYR 0.029 0.003 TYR D1004 PHE 0.041 0.003 PHE D1017 TRP 0.026 0.003 TRP A 462 HIS 0.031 0.003 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 9002) covalent geometry : angle 0.98807 (12257) SS BOND : bond 0.00505 ( 16) SS BOND : angle 1.29614 ( 32) hydrogen bonds : bond 0.05517 ( 194) hydrogen bonds : angle 7.50119 ( 495) Misc. bond : bond 0.00301 ( 4) link_ALPHA1-3 : bond 0.00597 ( 3) link_ALPHA1-3 : angle 2.97227 ( 9) link_ALPHA1-6 : bond 0.00659 ( 2) link_ALPHA1-6 : angle 2.68702 ( 6) link_BETA1-4 : bond 0.00860 ( 18) link_BETA1-4 : angle 3.50247 ( 54) link_BETA1-6 : bond 0.01246 ( 2) link_BETA1-6 : angle 3.30975 ( 6) link_NAG-ASN : bond 0.01154 ( 15) link_NAG-ASN : angle 4.30903 ( 45) *********************** 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 195 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.7579 (tp-100) cc_final: 0.7377 (tp-100) REVERT: A 207 GLU cc_start: 0.6210 (pm20) cc_final: 0.5941 (mp0) REVERT: A 317 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.4975 (pt) REVERT: A 469 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6133 (tp) REVERT: A 546 TYR cc_start: 0.4845 (m-80) cc_final: 0.4608 (m-80) outliers start: 33 outliers final: 15 residues processed: 178 average time/residue: 0.3690 time to fit residues: 72.5390 Evaluate side-chains 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 772 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 1 optimal weight: 0.0040 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS C 246 ASN A 310 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.226898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.209919 restraints weight = 17816.518| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 3.39 r_work: 0.4679 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9062 Z= 0.158 Angle : 0.893 16.406 12409 Z= 0.393 Chirality : 0.056 0.379 1453 Planarity : 0.005 0.065 1557 Dihedral : 12.459 100.314 1957 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.80 % Favored : 91.82 % Rotamer: Outliers : 2.29 % Allowed : 14.63 % Favored : 83.08 % 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: -1.96 (0.24), residues: 1064 helix: -0.99 (0.60), residues: 61 sheet: -0.78 (0.29), residues: 279 loop : -1.62 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 870 TYR 0.019 0.002 TYR A 331 PHE 0.030 0.002 PHE A 475 TRP 0.017 0.002 TRP A 255 HIS 0.008 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9002) covalent geometry : angle 0.82654 (12257) SS BOND : bond 0.00263 ( 16) SS BOND : angle 0.72741 ( 32) hydrogen bonds : bond 0.03799 ( 194) hydrogen bonds : angle 6.90333 ( 495) Misc. bond : bond 0.00642 ( 4) link_ALPHA1-3 : bond 0.00771 ( 3) link_ALPHA1-3 : angle 1.98383 ( 9) link_ALPHA1-6 : bond 0.00715 ( 2) link_ALPHA1-6 : angle 2.61105 ( 6) link_BETA1-4 : bond 0.00891 ( 18) link_BETA1-4 : angle 3.35657 ( 54) link_BETA1-6 : bond 0.00476 ( 2) link_BETA1-6 : angle 1.64484 ( 6) link_NAG-ASN : bond 0.01150 ( 15) link_NAG-ASN : angle 4.25410 ( 45) *********************** 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 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.6167 (pm20) cc_final: 0.5870 (mp0) REVERT: A 317 ILE cc_start: 0.5308 (OUTLIER) cc_final: 0.4875 (pp) REVERT: A 405 GLU cc_start: 0.5515 (mp0) cc_final: 0.4355 (tp30) REVERT: A 469 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5877 (tp) REVERT: A 582 ILE cc_start: 0.7483 (mp) cc_final: 0.6980 (tt) REVERT: A 693 PHE cc_start: 0.6961 (t80) cc_final: 0.6745 (t80) REVERT: A 694 ARG cc_start: 0.5400 (tmm160) cc_final: 0.5192 (ttp80) outliers start: 21 outliers final: 7 residues processed: 158 average time/residue: 0.3610 time to fit residues: 63.2500 Evaluate side-chains 149 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain D residue 977 CYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS C 76 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN D 978 GLN ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.226175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.209130 restraints weight = 17791.596| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 3.37 r_work: 0.4665 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9062 Z= 0.159 Angle : 0.873 16.763 12409 Z= 0.384 Chirality : 0.055 0.326 1453 Planarity : 0.005 0.065 1557 Dihedral : 11.569 94.534 1957 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.18 % Favored : 91.26 % Rotamer: Outliers : 2.40 % Allowed : 14.74 % Favored : 82.86 % 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: -2.00 (0.24), residues: 1064 helix: -1.00 (0.60), residues: 61 sheet: -0.76 (0.29), residues: 266 loop : -1.67 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 870 TYR 0.033 0.002 TYR A 499 PHE 0.028 0.002 PHE A 475 TRP 0.022 0.002 TRP A 255 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9002) covalent geometry : angle 0.80480 (12257) SS BOND : bond 0.00257 ( 16) SS BOND : angle 0.75926 ( 32) hydrogen bonds : bond 0.03709 ( 194) hydrogen bonds : angle 6.68533 ( 495) Misc. bond : bond 0.00488 ( 4) link_ALPHA1-3 : bond 0.00699 ( 3) link_ALPHA1-3 : angle 2.01740 ( 9) link_ALPHA1-6 : bond 0.00711 ( 2) link_ALPHA1-6 : angle 2.67561 ( 6) link_BETA1-4 : bond 0.00913 ( 18) link_BETA1-4 : angle 3.25526 ( 54) link_BETA1-6 : bond 0.00404 ( 2) link_BETA1-6 : angle 1.61478 ( 6) link_NAG-ASN : bond 0.01102 ( 15) link_NAG-ASN : angle 4.30057 ( 45) *********************** 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 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 PHE cc_start: 0.7055 (p90) cc_final: 0.6786 (p90) REVERT: A 207 GLU cc_start: 0.6163 (pm20) cc_final: 0.5874 (mp0) REVERT: A 317 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4765 (pp) REVERT: A 405 GLU cc_start: 0.5583 (mp0) cc_final: 0.4353 (tp30) REVERT: A 469 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6003 (tp) REVERT: A 693 PHE cc_start: 0.7019 (t80) cc_final: 0.6802 (t80) outliers start: 22 outliers final: 12 residues processed: 150 average time/residue: 0.3548 time to fit residues: 59.0550 Evaluate side-chains 148 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain D residue 977 CYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 769 HIS Chi-restraints excluded: chain A residue 772 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** 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 = 0.4912 r_free = 0.4912 target = 0.225773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.208513 restraints weight = 17805.992| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 3.45 r_work: 0.4656 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9062 Z= 0.156 Angle : 0.856 17.191 12409 Z= 0.378 Chirality : 0.054 0.310 1453 Planarity : 0.004 0.066 1557 Dihedral : 11.045 88.566 1957 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.89 % Favored : 91.64 % Rotamer: Outliers : 2.29 % Allowed : 15.07 % Favored : 82.64 % 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: -2.00 (0.24), residues: 1064 helix: -0.97 (0.62), residues: 61 sheet: -0.74 (0.31), residues: 259 loop : -1.67 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 870 TYR 0.024 0.002 TYR A 499 PHE 0.022 0.002 PHE A 475 TRP 0.021 0.002 TRP A 255 HIS 0.021 0.002 HIS A 769 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9002) covalent geometry : angle 0.79245 (12257) SS BOND : bond 0.00269 ( 16) SS BOND : angle 0.75697 ( 32) hydrogen bonds : bond 0.03628 ( 194) hydrogen bonds : angle 6.66968 ( 495) Misc. bond : bond 0.00186 ( 4) link_ALPHA1-3 : bond 0.00651 ( 3) link_ALPHA1-3 : angle 1.93247 ( 9) link_ALPHA1-6 : bond 0.00811 ( 2) link_ALPHA1-6 : angle 2.72358 ( 6) link_BETA1-4 : bond 0.00922 ( 18) link_BETA1-4 : angle 3.16389 ( 54) link_BETA1-6 : bond 0.00258 ( 2) link_BETA1-6 : angle 1.52142 ( 6) link_NAG-ASN : bond 0.01024 ( 15) link_NAG-ASN : angle 4.08306 ( 45) *********************** 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 158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 PHE cc_start: 0.7131 (p90) cc_final: 0.6854 (p90) REVERT: A 317 ILE cc_start: 0.5140 (OUTLIER) cc_final: 0.4742 (pp) REVERT: A 469 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6045 (tp) REVERT: A 546 TYR cc_start: 0.4077 (m-80) cc_final: 0.3706 (m-80) REVERT: A 582 ILE cc_start: 0.7475 (mp) cc_final: 0.7070 (tt) outliers start: 21 outliers final: 11 residues processed: 149 average time/residue: 0.3489 time to fit residues: 58.0266 Evaluate side-chains 145 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 597 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 49 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.226648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.209126 restraints weight = 17447.352| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 3.45 r_work: 0.4666 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9062 Z= 0.150 Angle : 0.864 17.150 12409 Z= 0.382 Chirality : 0.054 0.338 1453 Planarity : 0.005 0.088 1557 Dihedral : 10.689 81.301 1957 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.27 % Favored : 91.26 % Rotamer: Outliers : 2.18 % Allowed : 16.38 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.02 (0.25), residues: 1064 helix: -0.94 (0.62), residues: 61 sheet: -0.80 (0.31), residues: 248 loop : -1.66 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 872 TYR 0.024 0.002 TYR A 596 PHE 0.028 0.002 PHE A 475 TRP 0.043 0.002 TRP D 798 HIS 0.008 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9002) covalent geometry : angle 0.80469 (12257) SS BOND : bond 0.00345 ( 16) SS BOND : angle 0.79390 ( 32) hydrogen bonds : bond 0.03445 ( 194) hydrogen bonds : angle 6.62833 ( 495) Misc. bond : bond 0.00529 ( 4) link_ALPHA1-3 : bond 0.00645 ( 3) link_ALPHA1-3 : angle 1.79986 ( 9) link_ALPHA1-6 : bond 0.00863 ( 2) link_ALPHA1-6 : angle 2.74231 ( 6) link_BETA1-4 : bond 0.00915 ( 18) link_BETA1-4 : angle 3.09627 ( 54) link_BETA1-6 : bond 0.00164 ( 2) link_BETA1-6 : angle 1.41560 ( 6) link_NAG-ASN : bond 0.01054 ( 15) link_NAG-ASN : angle 3.95695 ( 45) *********************** 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 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.6170 (pm20) cc_final: 0.5866 (mp0) REVERT: A 317 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4770 (pp) REVERT: A 394 ILE cc_start: 0.6319 (pt) cc_final: 0.5873 (tt) REVERT: A 405 GLU cc_start: 0.5583 (mp0) cc_final: 0.4393 (tp30) REVERT: A 469 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6028 (tp) REVERT: A 582 ILE cc_start: 0.7409 (mp) cc_final: 0.7057 (tt) REVERT: A 660 ASN cc_start: 0.5814 (OUTLIER) cc_final: 0.5384 (m110) outliers start: 20 outliers final: 12 residues processed: 155 average time/residue: 0.3676 time to fit residues: 63.2126 Evaluate side-chains 153 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 660 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.227787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.210177 restraints weight = 17450.679| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 3.48 r_work: 0.4682 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9062 Z= 0.143 Angle : 0.907 25.898 12409 Z= 0.398 Chirality : 0.054 0.338 1453 Planarity : 0.005 0.090 1557 Dihedral : 10.223 69.225 1957 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.36 % Favored : 91.17 % Rotamer: Outliers : 1.86 % Allowed : 17.90 % Favored : 80.24 % 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: -1.97 (0.24), residues: 1064 helix: -0.90 (0.63), residues: 61 sheet: -0.68 (0.32), residues: 230 loop : -1.65 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 694 TYR 0.025 0.002 TYR A 596 PHE 0.031 0.002 PHE D 991 TRP 0.063 0.002 TRP D 798 HIS 0.008 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9002) covalent geometry : angle 0.85498 (12257) SS BOND : bond 0.00347 ( 16) SS BOND : angle 1.06798 ( 32) hydrogen bonds : bond 0.03220 ( 194) hydrogen bonds : angle 6.52034 ( 495) Misc. bond : bond 0.00847 ( 4) link_ALPHA1-3 : bond 0.00712 ( 3) link_ALPHA1-3 : angle 1.56342 ( 9) link_ALPHA1-6 : bond 0.01089 ( 2) link_ALPHA1-6 : angle 2.71530 ( 6) link_BETA1-4 : bond 0.00905 ( 18) link_BETA1-4 : angle 3.01686 ( 54) link_BETA1-6 : bond 0.00068 ( 2) link_BETA1-6 : angle 1.25140 ( 6) link_NAG-ASN : bond 0.01220 ( 15) link_NAG-ASN : angle 3.79568 ( 45) *********************** 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 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 MET cc_start: 0.4591 (mtt) cc_final: 0.4299 (mtt) REVERT: C 184 PHE cc_start: 0.7004 (p90) cc_final: 0.6670 (p90) REVERT: A 317 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4509 (pp) REVERT: A 394 ILE cc_start: 0.6246 (pt) cc_final: 0.5829 (tt) REVERT: A 469 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5885 (tp) REVERT: A 582 ILE cc_start: 0.7344 (mp) cc_final: 0.6998 (tt) REVERT: A 660 ASN cc_start: 0.5989 (OUTLIER) cc_final: 0.5314 (m110) REVERT: A 769 HIS cc_start: 0.4554 (OUTLIER) cc_final: 0.4333 (m170) outliers start: 17 outliers final: 11 residues processed: 155 average time/residue: 0.3562 time to fit residues: 61.4635 Evaluate side-chains 154 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 822 SER Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 769 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.225864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.208919 restraints weight = 17444.135| |-----------------------------------------------------------------------------| r_work (start): 0.4758 rms_B_bonded: 3.35 r_work: 0.4667 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9062 Z= 0.163 Angle : 0.914 22.208 12409 Z= 0.405 Chirality : 0.054 0.303 1453 Planarity : 0.005 0.089 1557 Dihedral : 10.134 58.644 1957 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.30 % Favored : 90.23 % Rotamer: Outliers : 2.07 % Allowed : 17.79 % Favored : 80.13 % 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: -2.00 (0.25), residues: 1064 helix: -0.91 (0.63), residues: 61 sheet: -0.71 (0.32), residues: 243 loop : -1.68 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 694 TYR 0.026 0.002 TYR A 596 PHE 0.023 0.002 PHE A 392 TRP 0.058 0.003 TRP D 798 HIS 0.015 0.002 HIS A 769 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9002) covalent geometry : angle 0.86104 (12257) SS BOND : bond 0.00324 ( 16) SS BOND : angle 0.95184 ( 32) hydrogen bonds : bond 0.03443 ( 194) hydrogen bonds : angle 6.58975 ( 495) Misc. bond : bond 0.00475 ( 4) link_ALPHA1-3 : bond 0.00523 ( 3) link_ALPHA1-3 : angle 1.77262 ( 9) link_ALPHA1-6 : bond 0.01227 ( 2) link_ALPHA1-6 : angle 2.84292 ( 6) link_BETA1-4 : bond 0.00920 ( 18) link_BETA1-4 : angle 3.02591 ( 54) link_BETA1-6 : bond 0.00098 ( 2) link_BETA1-6 : angle 1.12058 ( 6) link_NAG-ASN : bond 0.01069 ( 15) link_NAG-ASN : angle 3.85822 ( 45) *********************** 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 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 PHE cc_start: 0.7094 (p90) cc_final: 0.6754 (p90) REVERT: D 798 TRP cc_start: 0.5361 (OUTLIER) cc_final: 0.4803 (p90) REVERT: A 199 LYS cc_start: 0.8127 (tttt) cc_final: 0.7538 (tppt) REVERT: A 317 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4837 (pp) REVERT: A 394 ILE cc_start: 0.6340 (pt) cc_final: 0.5936 (tt) REVERT: A 419 GLU cc_start: 0.5283 (pt0) cc_final: 0.4995 (tm-30) REVERT: A 469 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6027 (tp) REVERT: A 582 ILE cc_start: 0.7471 (mp) cc_final: 0.7128 (tt) REVERT: A 660 ASN cc_start: 0.6300 (OUTLIER) cc_final: 0.5725 (m-40) outliers start: 19 outliers final: 12 residues processed: 156 average time/residue: 0.3712 time to fit residues: 64.5311 Evaluate side-chains 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 822 SER Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 660 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN A 647 HIS ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.227221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.209716 restraints weight = 17626.453| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 3.46 r_work: 0.4665 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9062 Z= 0.147 Angle : 0.890 19.420 12409 Z= 0.395 Chirality : 0.053 0.304 1453 Planarity : 0.005 0.088 1557 Dihedral : 9.887 58.620 1957 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.36 % Favored : 91.17 % Rotamer: Outliers : 2.40 % Allowed : 17.69 % Favored : 79.91 % 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: -2.03 (0.25), residues: 1064 helix: -0.95 (0.63), residues: 61 sheet: -0.76 (0.32), residues: 243 loop : -1.68 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 694 TYR 0.034 0.002 TYR A 596 PHE 0.028 0.002 PHE D 991 TRP 0.049 0.002 TRP D 798 HIS 0.006 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9002) covalent geometry : angle 0.83721 (12257) SS BOND : bond 0.00316 ( 16) SS BOND : angle 0.89536 ( 32) hydrogen bonds : bond 0.03279 ( 194) hydrogen bonds : angle 6.46356 ( 495) Misc. bond : bond 0.00413 ( 4) link_ALPHA1-3 : bond 0.00559 ( 3) link_ALPHA1-3 : angle 1.63358 ( 9) link_ALPHA1-6 : bond 0.01258 ( 2) link_ALPHA1-6 : angle 2.52438 ( 6) link_BETA1-4 : bond 0.00918 ( 18) link_BETA1-4 : angle 3.01733 ( 54) link_BETA1-6 : bond 0.00028 ( 2) link_BETA1-6 : angle 1.10757 ( 6) link_NAG-ASN : bond 0.01033 ( 15) link_NAG-ASN : angle 3.78739 ( 45) ********************** 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 159 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 MET cc_start: 0.4513 (mtt) cc_final: 0.4250 (mtt) REVERT: C 184 PHE cc_start: 0.7100 (p90) cc_final: 0.6820 (p90) REVERT: A 199 LYS cc_start: 0.8130 (tttt) cc_final: 0.7532 (tppt) REVERT: A 317 ILE cc_start: 0.5107 (OUTLIER) cc_final: 0.4731 (pp) REVERT: A 394 ILE cc_start: 0.6331 (pt) cc_final: 0.5937 (tt) REVERT: A 469 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6004 (tp) REVERT: A 582 ILE cc_start: 0.7461 (mp) cc_final: 0.7109 (tt) REVERT: A 636 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6563 (t-90) REVERT: A 660 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.6094 (m-40) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.3508 time to fit residues: 59.2774 Evaluate side-chains 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 822 SER Chi-restraints excluded: chain D residue 845 MET Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 660 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 1 optimal weight: 0.0000 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 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 = 0.4927 r_free = 0.4927 target = 0.228068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.210395 restraints weight = 17414.885| |-----------------------------------------------------------------------------| r_work (start): 0.4762 rms_B_bonded: 3.46 r_work: 0.4675 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9062 Z= 0.141 Angle : 0.880 17.088 12409 Z= 0.394 Chirality : 0.052 0.294 1453 Planarity : 0.005 0.087 1557 Dihedral : 9.540 59.394 1957 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.02 % Favored : 90.41 % Rotamer: Outliers : 2.51 % Allowed : 17.69 % Favored : 79.80 % 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: -2.05 (0.25), residues: 1064 helix: -0.95 (0.64), residues: 61 sheet: -0.81 (0.33), residues: 227 loop : -1.69 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 694 TYR 0.037 0.002 TYR A 596 PHE 0.023 0.002 PHE A 475 TRP 0.031 0.002 TRP D 798 HIS 0.006 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9002) covalent geometry : angle 0.82941 (12257) SS BOND : bond 0.00293 ( 16) SS BOND : angle 0.79736 ( 32) hydrogen bonds : bond 0.03115 ( 194) hydrogen bonds : angle 6.41099 ( 495) Misc. bond : bond 0.00376 ( 4) link_ALPHA1-3 : bond 0.00562 ( 3) link_ALPHA1-3 : angle 1.54111 ( 9) link_ALPHA1-6 : bond 0.01147 ( 2) link_ALPHA1-6 : angle 2.19036 ( 6) link_BETA1-4 : bond 0.00912 ( 18) link_BETA1-4 : angle 3.00417 ( 54) link_BETA1-6 : bond 0.00085 ( 2) link_BETA1-6 : angle 1.00352 ( 6) link_NAG-ASN : bond 0.01010 ( 15) link_NAG-ASN : angle 3.69625 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.43 seconds wall clock time: 57 minutes 21.11 seconds (3441.11 seconds total)