Starting phenix.real_space_refine on Sat Jun 7 13:44:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ziy_60133/06_2025/8ziy_60133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ziy_60133/06_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_60133/06_2025/8ziy_60133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ziy_60133/06_2025/8ziy_60133.map" model { file = "/net/cci-nas-00/data/ceres_data/8ziy_60133/06_2025/8ziy_60133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ziy_60133/06_2025/8ziy_60133.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.85, per 1000 atoms: 0.66 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: 3.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 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: 1.35 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: 3.81 Time building geometry restraints manager: 3.75 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: 1.050 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:16.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (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 TRP 0.006 0.000 TRP A 531 HIS 0.001 0.000 HIS C 96 PHE 0.007 0.001 PHE A 392 TYR 0.008 0.001 TYR A 276 ARG 0.004 0.000 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.05853 ( 15) link_NAG-ASN : angle 4.78010 ( 45) 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_ALPHA1-3 : bond 0.00337 ( 3) link_ALPHA1-3 : angle 1.72733 ( 9) hydrogen bonds : bond 0.24908 ( 194) hydrogen bonds : angle 10.02150 ( 495) link_BETA1-6 : bond 0.00444 ( 2) link_BETA1-6 : angle 0.85252 ( 6) SS BOND : bond 0.00122 ( 16) SS BOND : angle 0.49319 ( 32) covalent geometry : bond 0.00399 ( 9002) covalent geometry : angle 0.70781 (12257) Misc. bond : bond 0.00076 ( 4) *********************** 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 : 0.854 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: 0.3186 (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: 0.7704 time to fit residues: 153.1411 Evaluate side-chains 147 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 435 HIS A 569 GLN A 769 HIS A 779 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.231831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.214671 restraints weight = 17603.251| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 3.39 r_work: 0.4711 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9062 Z= 0.191 Angle : 0.892 12.092 12409 Z= 0.394 Chirality : 0.057 0.463 1453 Planarity : 0.005 0.060 1557 Dihedral : 16.307 112.159 1963 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.24 % Favored : 92.39 % Rotamer: Outliers : 3.06 % Allowed : 10.15 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1064 helix: -0.09 (0.66), residues: 61 sheet: 0.36 (0.30), residues: 287 loop : -1.08 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 216 HIS 0.007 0.001 HIS A 428 PHE 0.032 0.002 PHE A 392 TYR 0.024 0.002 TYR A 331 ARG 0.011 0.001 ARG D 830 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 15) link_NAG-ASN : angle 2.96546 ( 45) link_ALPHA1-6 : bond 0.00634 ( 2) link_ALPHA1-6 : angle 2.79425 ( 6) link_BETA1-4 : bond 0.00952 ( 18) link_BETA1-4 : angle 3.29744 ( 54) link_ALPHA1-3 : bond 0.00600 ( 3) link_ALPHA1-3 : angle 2.70495 ( 9) hydrogen bonds : bond 0.04653 ( 194) hydrogen bonds : angle 7.23754 ( 495) link_BETA1-6 : bond 0.00414 ( 2) link_BETA1-6 : angle 1.17378 ( 6) SS BOND : bond 0.00356 ( 16) SS BOND : angle 1.00149 ( 32) covalent geometry : bond 0.00399 ( 9002) covalent geometry : angle 0.84402 (12257) Misc. bond : bond 0.00359 ( 4) *********************** 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 191 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.907 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 98 GLN cc_start: 0.7262 (tp-100) cc_final: 0.7017 (tp-100) REVERT: C 182 ASN cc_start: 0.5189 (m-40) cc_final: 0.4248 (t0) REVERT: A 317 ILE cc_start: 0.5360 (OUTLIER) cc_final: 0.4836 (pt) REVERT: A 364 ASN cc_start: 0.6361 (OUTLIER) cc_final: 0.6027 (t0) REVERT: A 405 GLU cc_start: 0.5258 (mp0) cc_final: 0.4742 (tp30) REVERT: A 546 TYR cc_start: 0.4103 (m-80) cc_final: 0.3825 (m-80) REVERT: A 605 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7243 (p) outliers start: 28 outliers final: 9 residues processed: 172 average time/residue: 0.7547 time to fit residues: 143.4176 Evaluate side-chains 156 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 364 ASN 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 10 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.230452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.212947 restraints weight = 17836.846| |-----------------------------------------------------------------------------| r_work (start): 0.4796 rms_B_bonded: 3.49 r_work: 0.4705 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9062 Z= 0.178 Angle : 0.878 13.962 12409 Z= 0.383 Chirality : 0.056 0.364 1453 Planarity : 0.005 0.061 1557 Dihedral : 13.984 109.038 1957 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.14 % Favored : 92.48 % Rotamer: Outliers : 2.18 % Allowed : 12.88 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.25), residues: 1064 helix: -0.64 (0.63), residues: 60 sheet: -0.10 (0.29), residues: 275 loop : -1.27 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 216 HIS 0.005 0.001 HIS A 428 PHE 0.039 0.002 PHE D1017 TYR 0.019 0.002 TYR D1004 ARG 0.007 0.001 ARG D 870 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 15) link_NAG-ASN : angle 3.81086 ( 45) link_ALPHA1-6 : bond 0.00592 ( 2) link_ALPHA1-6 : angle 2.36305 ( 6) link_BETA1-4 : bond 0.00921 ( 18) link_BETA1-4 : angle 3.29967 ( 54) link_ALPHA1-3 : bond 0.00676 ( 3) link_ALPHA1-3 : angle 2.27884 ( 9) hydrogen bonds : bond 0.04245 ( 194) hydrogen bonds : angle 7.04789 ( 495) link_BETA1-6 : bond 0.00863 ( 2) link_BETA1-6 : angle 1.98715 ( 6) SS BOND : bond 0.00303 ( 16) SS BOND : angle 0.91976 ( 32) covalent geometry : bond 0.00374 ( 9002) covalent geometry : angle 0.81716 (12257) Misc. bond : bond 0.00212 ( 4) *********************** 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 172 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 ASN cc_start: 0.5109 (m-40) cc_final: 0.4351 (t0) REVERT: A 317 ILE cc_start: 0.5179 (OUTLIER) cc_final: 0.4769 (pt) REVERT: A 405 GLU cc_start: 0.5513 (mp0) cc_final: 0.4845 (tp30) outliers start: 20 outliers final: 8 residues processed: 163 average time/residue: 1.1524 time to fit residues: 206.9365 Evaluate side-chains 153 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** A 443 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.230240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.212548 restraints weight = 17743.471| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 3.51 r_work: 0.4700 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.3339 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= 0.149 Angle : 0.851 17.719 12409 Z= 0.373 Chirality : 0.056 0.447 1453 Planarity : 0.004 0.061 1557 Dihedral : 12.286 102.604 1957 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.80 % Favored : 91.73 % Rotamer: Outliers : 3.17 % Allowed : 12.88 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.25), residues: 1064 helix: -0.69 (0.63), residues: 60 sheet: -0.50 (0.29), residues: 287 loop : -1.42 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 255 HIS 0.009 0.001 HIS C 96 PHE 0.031 0.002 PHE A 475 TYR 0.031 0.002 TYR A 499 ARG 0.011 0.001 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00900 ( 15) link_NAG-ASN : angle 4.24137 ( 45) link_ALPHA1-6 : bond 0.00739 ( 2) link_ALPHA1-6 : angle 2.57396 ( 6) link_BETA1-4 : bond 0.00925 ( 18) link_BETA1-4 : angle 3.20243 ( 54) link_ALPHA1-3 : bond 0.00809 ( 3) link_ALPHA1-3 : angle 2.02347 ( 9) hydrogen bonds : bond 0.03700 ( 194) hydrogen bonds : angle 6.70207 ( 495) link_BETA1-6 : bond 0.00391 ( 2) link_BETA1-6 : angle 1.59961 ( 6) SS BOND : bond 0.00270 ( 16) SS BOND : angle 0.78770 ( 32) covalent geometry : bond 0.00321 ( 9002) covalent geometry : angle 0.78255 (12257) Misc. bond : bond 0.00064 ( 4) *********************** 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 179 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.947 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 182 ASN cc_start: 0.5042 (m-40) cc_final: 0.4315 (t0) REVERT: A 317 ILE cc_start: 0.5102 (OUTLIER) cc_final: 0.4751 (pt) REVERT: A 394 ILE cc_start: 0.6482 (mt) cc_final: 0.6240 (tt) REVERT: A 405 GLU cc_start: 0.5379 (mp0) cc_final: 0.4729 (tp30) REVERT: A 469 LEU cc_start: 0.6313 (mm) cc_final: 0.5699 (tp) REVERT: A 581 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5418 (mt-10) REVERT: A 694 ARG cc_start: 0.6019 (ttp80) cc_final: 0.5619 (ttp80) outliers start: 29 outliers final: 12 residues processed: 164 average time/residue: 0.7698 time to fit residues: 139.8714 Evaluate side-chains 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 111 ILE 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 453 GLN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 772 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.0370 chunk 13 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN D 978 GLN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** 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 = 0.4944 r_free = 0.4944 target = 0.230189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.212796 restraints weight = 17454.992| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 3.42 r_work: 0.4700 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9062 Z= 0.141 Angle : 0.828 17.320 12409 Z= 0.363 Chirality : 0.053 0.325 1453 Planarity : 0.004 0.062 1557 Dihedral : 11.275 95.423 1957 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.42 % Favored : 92.01 % Rotamer: Outliers : 2.07 % Allowed : 14.41 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 1064 helix: -0.65 (0.65), residues: 60 sheet: -0.52 (0.29), residues: 287 loop : -1.50 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 255 HIS 0.008 0.001 HIS C 63 PHE 0.029 0.002 PHE A 475 TYR 0.022 0.002 TYR A 596 ARG 0.029 0.001 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.01092 ( 15) link_NAG-ASN : angle 4.13854 ( 45) link_ALPHA1-6 : bond 0.00799 ( 2) link_ALPHA1-6 : angle 2.65472 ( 6) link_BETA1-4 : bond 0.00902 ( 18) link_BETA1-4 : angle 3.09135 ( 54) link_ALPHA1-3 : bond 0.00812 ( 3) link_ALPHA1-3 : angle 1.82073 ( 9) hydrogen bonds : bond 0.03338 ( 194) hydrogen bonds : angle 6.47830 ( 495) link_BETA1-6 : bond 0.00164 ( 2) link_BETA1-6 : angle 1.48234 ( 6) SS BOND : bond 0.00236 ( 16) SS BOND : angle 0.73222 ( 32) covalent geometry : bond 0.00302 ( 9002) covalent geometry : angle 0.76212 (12257) Misc. bond : bond 0.00365 ( 4) *********************** 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 172 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.925 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 98 GLN cc_start: 0.7446 (tp-100) cc_final: 0.7181 (tp-100) REVERT: C 182 ASN cc_start: 0.4938 (m-40) cc_final: 0.4163 (t0) REVERT: D 828 TYR cc_start: 0.6626 (t80) cc_final: 0.6318 (t80) REVERT: A 207 GLU cc_start: 0.6019 (pm20) cc_final: 0.5811 (mp0) REVERT: A 317 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4819 (pp) REVERT: A 405 GLU cc_start: 0.5072 (mp0) cc_final: 0.4506 (tp30) REVERT: A 469 LEU cc_start: 0.6370 (mm) cc_final: 0.5828 (tp) REVERT: A 581 GLU cc_start: 0.5760 (mt-10) cc_final: 0.5480 (mt-10) outliers start: 19 outliers final: 10 residues processed: 162 average time/residue: 0.7370 time to fit residues: 132.2567 Evaluate side-chains 157 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 111 ILE 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 453 GLN Chi-restraints excluded: chain A residue 769 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 55 optimal weight: 0.2980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.229893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.212406 restraints weight = 17506.780| |-----------------------------------------------------------------------------| r_work (start): 0.4782 rms_B_bonded: 3.44 r_work: 0.4695 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.3835 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= 0.145 Angle : 0.840 17.324 12409 Z= 0.370 Chirality : 0.053 0.369 1453 Planarity : 0.004 0.062 1557 Dihedral : 10.784 88.965 1957 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.52 % Favored : 91.92 % Rotamer: Outliers : 2.29 % Allowed : 15.39 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.25), residues: 1064 helix: -0.70 (0.65), residues: 61 sheet: -0.27 (0.31), residues: 253 loop : -1.53 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 255 HIS 0.021 0.002 HIS A 769 PHE 0.026 0.002 PHE A 475 TYR 0.025 0.002 TYR A 596 ARG 0.018 0.001 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00943 ( 15) link_NAG-ASN : angle 4.04412 ( 45) link_ALPHA1-6 : bond 0.00512 ( 2) link_ALPHA1-6 : angle 2.58083 ( 6) link_BETA1-4 : bond 0.00924 ( 18) link_BETA1-4 : angle 2.98659 ( 54) link_ALPHA1-3 : bond 0.00765 ( 3) link_ALPHA1-3 : angle 1.86600 ( 9) hydrogen bonds : bond 0.03312 ( 194) hydrogen bonds : angle 6.49698 ( 495) link_BETA1-6 : bond 0.00364 ( 2) link_BETA1-6 : angle 1.38679 ( 6) SS BOND : bond 0.00360 ( 16) SS BOND : angle 0.87220 ( 32) covalent geometry : bond 0.00313 ( 9002) covalent geometry : angle 0.77865 (12257) Misc. bond : bond 0.00314 ( 4) *********************** 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 170 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.885 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: 0.7501 (tp-100) cc_final: 0.7233 (tp-100) REVERT: C 182 ASN cc_start: 0.5001 (m-40) cc_final: 0.4169 (t0) REVERT: C 183 MET cc_start: 0.4675 (mtt) cc_final: 0.4398 (mtt) REVERT: A 207 GLU cc_start: 0.6028 (pm20) cc_final: 0.5794 (mp0) REVERT: A 317 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4713 (pp) REVERT: A 405 GLU cc_start: 0.5195 (mp0) cc_final: 0.4589 (tp30) REVERT: A 469 LEU cc_start: 0.6565 (mm) cc_final: 0.5999 (tp) outliers start: 21 outliers final: 14 residues processed: 162 average time/residue: 0.7259 time to fit residues: 130.9452 Evaluate side-chains 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS 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 817 SER Chi-restraints excluded: chain D residue 822 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 597 THR Chi-restraints excluded: chain A residue 636 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** A 310 GLN A 346 ASN ** A 443 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 = 0.4926 r_free = 0.4926 target = 0.228003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.211190 restraints weight = 17588.261| |-----------------------------------------------------------------------------| r_work (start): 0.4773 rms_B_bonded: 3.30 r_work: 0.4685 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.4059 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= 0.148 Angle : 0.844 17.910 12409 Z= 0.373 Chirality : 0.053 0.346 1453 Planarity : 0.004 0.063 1557 Dihedral : 10.513 83.473 1957 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.80 % Favored : 91.73 % Rotamer: Outliers : 2.29 % Allowed : 16.05 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.25), residues: 1064 helix: -0.83 (0.64), residues: 61 sheet: -0.45 (0.29), residues: 270 loop : -1.59 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 796 HIS 0.006 0.001 HIS C 63 PHE 0.029 0.002 PHE D 991 TYR 0.021 0.002 TYR A 596 ARG 0.015 0.001 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00988 ( 15) link_NAG-ASN : angle 3.97907 ( 45) link_ALPHA1-6 : bond 0.00808 ( 2) link_ALPHA1-6 : angle 2.80725 ( 6) link_BETA1-4 : bond 0.00902 ( 18) link_BETA1-4 : angle 2.96195 ( 54) link_ALPHA1-3 : bond 0.00723 ( 3) link_ALPHA1-3 : angle 1.83374 ( 9) hydrogen bonds : bond 0.03379 ( 194) hydrogen bonds : angle 6.47006 ( 495) link_BETA1-6 : bond 0.00245 ( 2) link_BETA1-6 : angle 1.44395 ( 6) SS BOND : bond 0.00266 ( 16) SS BOND : angle 0.92800 ( 32) covalent geometry : bond 0.00320 ( 9002) covalent geometry : angle 0.78356 (12257) Misc. bond : bond 0.00348 ( 4) *********************** 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 173 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.960 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 98 GLN cc_start: 0.7506 (tp-100) cc_final: 0.7285 (tp-100) REVERT: C 182 ASN cc_start: 0.4987 (m-40) cc_final: 0.4152 (t0) REVERT: C 183 MET cc_start: 0.4760 (mtt) cc_final: 0.4521 (mtt) REVERT: D 1004 TYR cc_start: 0.6280 (m-10) cc_final: 0.6027 (m-10) REVERT: A 207 GLU cc_start: 0.5973 (pm20) cc_final: 0.5736 (mp0) REVERT: A 317 ILE cc_start: 0.5304 (OUTLIER) cc_final: 0.4932 (pp) REVERT: A 405 GLU cc_start: 0.5220 (mp0) cc_final: 0.4585 (tp30) REVERT: A 469 LEU cc_start: 0.6563 (mm) cc_final: 0.6101 (tp) REVERT: A 475 PHE cc_start: 0.5802 (p90) cc_final: 0.5518 (p90) outliers start: 21 outliers final: 13 residues processed: 164 average time/residue: 0.8046 time to fit residues: 145.6712 Evaluate side-chains 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS 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 817 SER Chi-restraints excluded: chain D residue 822 SER 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 342 TYR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 636 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 96 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.226996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.209787 restraints weight = 17859.873| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 3.43 r_work: 0.4666 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9062 Z= 0.161 Angle : 0.904 28.571 12409 Z= 0.397 Chirality : 0.054 0.392 1453 Planarity : 0.005 0.063 1557 Dihedral : 10.307 75.018 1957 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.99 % Favored : 91.54 % Rotamer: Outliers : 2.29 % Allowed : 16.48 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 1064 helix: -0.88 (0.64), residues: 61 sheet: -0.59 (0.30), residues: 268 loop : -1.64 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 255 HIS 0.010 0.001 HIS C 63 PHE 0.022 0.002 PHE A 475 TYR 0.021 0.002 TYR A 331 ARG 0.013 0.001 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.01154 ( 15) link_NAG-ASN : angle 4.38481 ( 45) link_ALPHA1-6 : bond 0.00876 ( 2) link_ALPHA1-6 : angle 2.83015 ( 6) link_BETA1-4 : bond 0.00899 ( 18) link_BETA1-4 : angle 2.93964 ( 54) link_ALPHA1-3 : bond 0.00649 ( 3) link_ALPHA1-3 : angle 1.79808 ( 9) hydrogen bonds : bond 0.03387 ( 194) hydrogen bonds : angle 6.31279 ( 495) link_BETA1-6 : bond 0.00244 ( 2) link_BETA1-6 : angle 1.44229 ( 6) SS BOND : bond 0.00478 ( 16) SS BOND : angle 1.32204 ( 32) covalent geometry : bond 0.00347 ( 9002) covalent geometry : angle 0.84059 (12257) Misc. bond : bond 0.00554 ( 4) *********************** 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 167 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.892 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 182 ASN cc_start: 0.5092 (m-40) cc_final: 0.4258 (t0) REVERT: C 184 PHE cc_start: 0.7054 (p90) cc_final: 0.6723 (p90) REVERT: A 207 GLU cc_start: 0.5956 (pm20) cc_final: 0.5736 (mp0) REVERT: A 317 ILE cc_start: 0.5380 (OUTLIER) cc_final: 0.4912 (pp) REVERT: A 405 GLU cc_start: 0.5279 (mp0) cc_final: 0.4650 (tp30) REVERT: A 469 LEU cc_start: 0.6633 (mm) cc_final: 0.6184 (tp) REVERT: A 475 PHE cc_start: 0.5820 (p90) cc_final: 0.5525 (p90) outliers start: 21 outliers final: 15 residues processed: 156 average time/residue: 0.7584 time to fit residues: 131.0035 Evaluate side-chains 160 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 817 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 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 636 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 0.3980 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 0.0170 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.227574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.210332 restraints weight = 17732.359| |-----------------------------------------------------------------------------| r_work (start): 0.4762 rms_B_bonded: 3.40 r_work: 0.4675 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9062 Z= 0.158 Angle : 0.903 20.412 12409 Z= 0.404 Chirality : 0.056 0.642 1453 Planarity : 0.005 0.081 1557 Dihedral : 10.047 63.590 1957 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.55 % Favored : 90.98 % Rotamer: Outliers : 1.86 % Allowed : 16.92 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.25), residues: 1064 helix: -0.90 (0.64), residues: 61 sheet: -0.63 (0.30), residues: 269 loop : -1.63 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 798 HIS 0.007 0.001 HIS C 96 PHE 0.021 0.002 PHE A 475 TYR 0.018 0.001 TYR A 331 ARG 0.012 0.001 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.01367 ( 15) link_NAG-ASN : angle 4.20843 ( 45) link_ALPHA1-6 : bond 0.00981 ( 2) link_ALPHA1-6 : angle 2.75230 ( 6) link_BETA1-4 : bond 0.00882 ( 18) link_BETA1-4 : angle 2.92764 ( 54) link_ALPHA1-3 : bond 0.00654 ( 3) link_ALPHA1-3 : angle 1.68596 ( 9) hydrogen bonds : bond 0.03311 ( 194) hydrogen bonds : angle 6.27463 ( 495) link_BETA1-6 : bond 0.00200 ( 2) link_BETA1-6 : angle 1.33075 ( 6) SS BOND : bond 0.00316 ( 16) SS BOND : angle 1.30409 ( 32) covalent geometry : bond 0.00347 ( 9002) covalent geometry : angle 0.84374 (12257) Misc. bond : bond 0.00622 ( 4) *********************** 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 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.916 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 182 ASN cc_start: 0.5018 (m-40) cc_final: 0.4208 (t0) REVERT: C 184 PHE cc_start: 0.7086 (p90) cc_final: 0.6789 (p90) REVERT: A 258 ARG cc_start: 0.4903 (tmm160) cc_final: 0.4668 (tmm160) REVERT: A 317 ILE cc_start: 0.5266 (OUTLIER) cc_final: 0.4907 (pp) REVERT: A 405 GLU cc_start: 0.5319 (mp0) cc_final: 0.4676 (tp30) REVERT: A 469 LEU cc_start: 0.6624 (mm) cc_final: 0.6203 (tp) REVERT: A 475 PHE cc_start: 0.5804 (p90) cc_final: 0.5522 (p90) REVERT: A 636 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6355 (t-90) outliers start: 17 outliers final: 13 residues processed: 155 average time/residue: 0.7125 time to fit residues: 122.7434 Evaluate side-chains 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL 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 817 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 317 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 769 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 HIS ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN A 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.227559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.210765 restraints weight = 17459.257| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 3.28 r_work: 0.4684 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.4606 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= 0.161 Angle : 0.928 22.729 12409 Z= 0.418 Chirality : 0.057 0.610 1453 Planarity : 0.005 0.067 1557 Dihedral : 9.830 58.812 1957 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.18 % Favored : 91.35 % Rotamer: Outliers : 1.53 % Allowed : 17.47 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.25), residues: 1064 helix: -0.97 (0.64), residues: 61 sheet: -0.63 (0.31), residues: 254 loop : -1.69 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP D 798 HIS 0.007 0.001 HIS C 96 PHE 0.022 0.002 PHE A 475 TYR 0.026 0.002 TYR A 596 ARG 0.015 0.001 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.01300 ( 15) link_NAG-ASN : angle 4.12502 ( 45) link_ALPHA1-6 : bond 0.01192 ( 2) link_ALPHA1-6 : angle 2.66902 ( 6) link_BETA1-4 : bond 0.00909 ( 18) link_BETA1-4 : angle 2.90229 ( 54) link_ALPHA1-3 : bond 0.00564 ( 3) link_ALPHA1-3 : angle 1.64852 ( 9) hydrogen bonds : bond 0.03229 ( 194) hydrogen bonds : angle 6.32622 ( 495) link_BETA1-6 : bond 0.00102 ( 2) link_BETA1-6 : angle 1.25441 ( 6) SS BOND : bond 0.00316 ( 16) SS BOND : angle 1.07218 ( 32) covalent geometry : bond 0.00349 ( 9002) covalent geometry : angle 0.87339 (12257) Misc. bond : bond 0.00770 ( 4) ********************** 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: 14 poor density : 145 time to evaluate : 0.871 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 182 ASN cc_start: 0.4961 (m-40) cc_final: 0.4212 (t0) REVERT: C 184 PHE cc_start: 0.7128 (p90) cc_final: 0.6793 (p90) REVERT: A 258 ARG cc_start: 0.4940 (tmm160) cc_final: 0.4653 (tmm160) REVERT: A 317 ILE cc_start: 0.5130 (OUTLIER) cc_final: 0.4761 (pp) REVERT: A 405 GLU cc_start: 0.5232 (mp0) cc_final: 0.4619 (tp30) REVERT: A 469 LEU cc_start: 0.6641 (mm) cc_final: 0.6217 (tp) REVERT: A 546 TYR cc_start: 0.4468 (m-80) cc_final: 0.4223 (m-80) REVERT: A 636 HIS cc_start: 0.6627 (OUTLIER) cc_final: 0.6331 (t-90) outliers start: 14 outliers final: 11 residues processed: 155 average time/residue: 0.9158 time to fit residues: 158.1855 Evaluate side-chains 158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 895 ILE Chi-restraints excluded: chain D residue 950 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 453 GLN Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 636 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 978 GLN ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN A 647 HIS A 769 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.227957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.211163 restraints weight = 17568.907| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 3.28 r_work: 0.4684 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9062 Z= 0.159 Angle : 0.912 18.022 12409 Z= 0.414 Chirality : 0.056 0.562 1453 Planarity : 0.005 0.063 1557 Dihedral : 9.710 59.731 1957 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.55 % Favored : 90.98 % Rotamer: Outliers : 1.31 % Allowed : 18.34 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1064 helix: -0.88 (0.65), residues: 61 sheet: -0.79 (0.30), residues: 266 loop : -1.70 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 796 HIS 0.007 0.001 HIS C 96 PHE 0.021 0.002 PHE A 475 TYR 0.035 0.002 TYR C 229 ARG 0.012 0.001 ARG D 872 Details of bonding type rmsd link_NAG-ASN : bond 0.01278 ( 15) link_NAG-ASN : angle 4.11902 ( 45) link_ALPHA1-6 : bond 0.01220 ( 2) link_ALPHA1-6 : angle 2.56409 ( 6) link_BETA1-4 : bond 0.00889 ( 18) link_BETA1-4 : angle 2.91194 ( 54) link_ALPHA1-3 : bond 0.00561 ( 3) link_ALPHA1-3 : angle 1.66216 ( 9) hydrogen bonds : bond 0.03256 ( 194) hydrogen bonds : angle 6.43424 ( 495) link_BETA1-6 : bond 0.00049 ( 2) link_BETA1-6 : angle 1.19648 ( 6) SS BOND : bond 0.00243 ( 16) SS BOND : angle 0.95065 ( 32) covalent geometry : bond 0.00347 ( 9002) covalent geometry : angle 0.85695 (12257) Misc. bond : bond 0.00503 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7025.95 seconds wall clock time: 122 minutes 42.00 seconds (7362.00 seconds total)