Starting phenix.real_space_refine on Wed Sep 17 12:42:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zj4_60137/09_2025/8zj4_60137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zj4_60137/09_2025/8zj4_60137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zj4_60137/09_2025/8zj4_60137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zj4_60137/09_2025/8zj4_60137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zj4_60137/09_2025/8zj4_60137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zj4_60137/09_2025/8zj4_60137.map" } resolution = 2.67 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= 0.026 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 5471 2.51 5 N 1420 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8734 Number of models: 1 Model: "" Number of chains: 15 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: "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: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4690 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "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: "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: 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 Time building chain proxies: 2.25, per 1000 atoms: 0.26 Number of scatterers: 8734 At special positions: 0 Unit cell: (85.744, 109.044, 155.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1787 8.00 N 1420 7.00 C 5471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 826 " distance=2.03 Simple disulfide: pdb=" SG CYS D 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 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 A 184 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 422 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 2 " - " BMA M 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 801 " - " ASN A 682 " " NAG A 802 " - " ASN A 503 " " 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 A 725 " " NAG H 1 " - " ASN A 534 " " NAG I 1 " - " ASN A 630 " " NAG J 1 " - " ASN A 335 " " NAG K 1 " - " ASN A 388 " " NAG L 1 " - " ASN A 440 " " NAG M 1 " - " ASN A 470 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 331.5 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: 13 helices and 14 sheets defined 8.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'D' and resid 825 through 828 Processing helix chain 'D' and resid 833 through 835 No H-bonds generated for 'chain 'D' and resid 833 through 835' Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.570A pdb=" N GLN D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1019 removed outlier: 3.648A pdb=" N PHE D1017 " --> pdb=" O TRP D1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.919A pdb=" N ASN C 33 " --> pdb=" O CYS C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 4.203A pdb=" N TYR C 65 " --> pdb=" O GLY C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 235 through 246 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 Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.518A pdb=" N ILE A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 removed outlier: 4.016A pdb=" N GLU A 674 " --> pdb=" O GLY A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 Processing sheet with id=AA1, first strand: chain 'D' and resid 789 through 790 removed outlier: 3.849A pdb=" N CYS D 956 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 913 " --> pdb=" O PRO D 974 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 799 through 804 removed outlier: 3.797A pdb=" N CYS D 810 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR D 804 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY D 811 " --> pdb=" O ALA D 823 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA D 823 " --> pdb=" O GLY D 811 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU D 861 " --> pdb=" O HIS D 881 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TRP D 837 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 42 removed outlier: 4.008A pdb=" N CYS C 48 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 110 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE C 93 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 112 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.699A pdb=" N CYS C 139 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 204 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL C 214 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR C 230 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP C 216 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 190 Processing sheet with id=AA6, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.837A pdb=" N LEU A 280 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.636A pdb=" N VAL A 357 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A 452 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 370 removed outlier: 13.106A pdb=" N PHE A 392 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP A 494 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 394 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A 492 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS A 428 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP A 494 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP A 426 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 538 removed outlier: 3.670A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS A 628 " --> pdb=" O GLN A 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.674A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 580 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 595 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 582 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.831A pdb=" N VAL A 605 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 678 through 681 Processing sheet with id=AB5, first strand: chain 'A' and resid 740 through 742 203 hydrogen bonds defined for protein. 522 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: 1.57 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1455 1.29 - 1.42: 2331 1.42 - 1.56: 5081 1.56 - 1.69: 4 1.69 - 1.82: 68 Bond restraints: 8939 Sorted by residual: bond pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " ideal model delta sigma weight residual 1.524 1.439 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.413 1.495 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C2 BMA E 3 " pdb=" C3 BMA E 3 " ideal model delta sigma weight residual 1.544 1.465 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C3 BMA E 3 " pdb=" C4 BMA E 3 " ideal model delta sigma weight residual 1.541 1.468 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C6 NAG E 1 " pdb=" O6 NAG E 1 " ideal model delta sigma weight residual 1.408 1.480 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 8934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.48: 12100 4.48 - 8.97: 63 8.97 - 13.45: 4 13.45 - 17.94: 2 17.94 - 22.42: 2 Bond angle restraints: 12171 Sorted by residual: angle pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 110.79 88.37 22.42 3.00e+00 1.11e-01 5.59e+01 angle pdb=" C6 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 108.73 130.15 -21.42 3.00e+00 1.11e-01 5.10e+01 angle pdb=" C3 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 110.74 93.05 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" C5 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sigma weight residual 111.70 129.10 -17.40 3.00e+00 1.11e-01 3.37e+01 angle pdb=" CA ASN D 909 " pdb=" CB ASN D 909 " pdb=" CG ASN D 909 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 ... (remaining 12166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 5505 23.46 - 46.92: 118 46.92 - 70.38: 39 70.38 - 93.84: 58 93.84 - 117.30: 37 Dihedral angle restraints: 5757 sinusoidal: 2700 harmonic: 3057 Sorted by residual: dihedral pdb=" C ASN D 909 " pdb=" N ASN D 909 " pdb=" CA ASN D 909 " pdb=" CB ASN D 909 " ideal model delta harmonic sigma weight residual -122.60 -134.96 12.36 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" CB CYS A 716 " pdb=" SG CYS A 716 " pdb=" SG CYS A 767 " pdb=" CB CYS A 767 " ideal model delta sinusoidal sigma weight residual 93.00 126.67 -33.67 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" C2 MAN L 4 " pdb=" C1 MAN L 4 " pdb=" O5 MAN L 4 " pdb=" C5 MAN L 4 " ideal model delta sinusoidal sigma weight residual -57.62 59.68 -117.30 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 5754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 1414 0.216 - 0.431: 10 0.431 - 0.647: 2 0.647 - 0.863: 1 0.863 - 1.079: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C5 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" C6 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.41 -1.33 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.70 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG E 2 " pdb=" O6 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 ... (remaining 1425 not shown) Planarity restraints: 1567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.305 2.00e-02 2.50e+03 2.58e-01 8.31e+02 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.450 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.240 2.00e-02 2.50e+03 2.04e-01 5.20e+02 pdb=" C7 NAG E 1 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.350 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 909 " -0.001 2.00e-02 2.50e+03 5.12e-02 3.27e+01 pdb=" CG ASN D 909 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN D 909 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 909 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.057 2.00e-02 2.50e+03 ... (remaining 1564 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 163 2.65 - 3.21: 7647 3.21 - 3.77: 13182 3.77 - 4.34: 18054 4.34 - 4.90: 29472 Nonbonded interactions: 68518 Sorted by model distance: nonbonded pdb=" O3 NAG E 1 " pdb=" O7 NAG E 1 " model vdw 2.083 3.040 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.168 3.040 nonbonded pdb=" O4 NAG E 2 " pdb=" O6 NAG E 2 " model vdw 2.179 3.040 nonbonded pdb=" O3 NAG K 2 " pdb=" O2 BMA K 3 " model vdw 2.213 3.040 nonbonded pdb=" OG SER A 727 " pdb=" O ARG A 764 " model vdw 2.247 3.040 ... (remaining 68513 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 'I' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'H' 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.600 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: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4710 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 0.085 8989 Z= 0.249 Angle : 0.946 26.519 12306 Z= 0.383 Chirality : 0.066 1.079 1428 Planarity : 0.009 0.258 1554 Dihedral : 17.141 117.298 3760 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 2.07 % Allowed : 2.51 % Favored : 95.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.27), residues: 1064 helix: 1.21 (0.70), residues: 67 sheet: 0.44 (0.33), residues: 271 loop : -0.58 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 368 TYR 0.006 0.001 TYR A 276 PHE 0.007 0.001 PHE C 184 TRP 0.005 0.001 TRP C 57 HIS 0.001 0.000 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8939) covalent geometry : angle 0.80815 (12171) SS BOND : bond 0.00096 ( 15) SS BOND : angle 0.60373 ( 30) hydrogen bonds : bond 0.14815 ( 203) hydrogen bonds : angle 6.45798 ( 522) link_ALPHA1-3 : bond 0.00611 ( 2) link_ALPHA1-3 : angle 1.44584 ( 6) link_ALPHA1-6 : bond 0.00359 ( 1) link_ALPHA1-6 : angle 1.48973 ( 3) link_BETA1-4 : bond 0.01201 ( 13) link_BETA1-4 : angle 4.58521 ( 39) link_BETA1-6 : bond 0.00463 ( 6) link_BETA1-6 : angle 4.11653 ( 18) link_NAG-ASN : bond 0.00628 ( 13) link_NAG-ASN : angle 7.00399 ( 39) *********************** 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 169 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.363 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: symmetry clash revert: symmetry clash REVERT: A 356 TRP cc_start: 0.6209 (m100) cc_final: 0.5431 (m100) REVERT: A 546 TYR cc_start: 0.5152 (p90) cc_final: 0.4916 (p90) outliers start: 19 outliers final: 6 residues processed: 165 average time/residue: 0.3030 time to fit residues: 55.8395 Evaluate side-chains 137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN D 981 ASN D1015 GLN C 38 GLN C 56 GLN C 86 GLN C 159 GLN C 222 GLN C 234 ASN A 310 GLN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN A 435 HIS A 559 GLN A 575 ASN A 647 HIS ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.248082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.231969 restraints weight = 18181.314| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 3.15 r_work: 0.4800 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5151 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8989 Z= 0.241 Angle : 0.985 14.037 12306 Z= 0.445 Chirality : 0.056 0.571 1428 Planarity : 0.005 0.054 1554 Dihedral : 16.140 103.280 1862 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.83 % Favored : 90.98 % Rotamer: Outliers : 3.82 % Allowed : 8.73 % Favored : 87.45 % 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: -0.96 (0.26), residues: 1064 helix: -0.21 (0.66), residues: 63 sheet: 0.10 (0.31), residues: 298 loop : -1.04 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 830 TYR 0.023 0.003 TYR D1004 PHE 0.018 0.002 PHE A 386 TRP 0.024 0.003 TRP A 356 HIS 0.014 0.003 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8939) covalent geometry : angle 0.91560 (12171) SS BOND : bond 0.00460 ( 15) SS BOND : angle 1.56578 ( 30) hydrogen bonds : bond 0.04460 ( 203) hydrogen bonds : angle 6.54820 ( 522) link_ALPHA1-3 : bond 0.00803 ( 2) link_ALPHA1-3 : angle 2.92859 ( 6) link_ALPHA1-6 : bond 0.00331 ( 1) link_ALPHA1-6 : angle 1.69724 ( 3) link_BETA1-4 : bond 0.00972 ( 13) link_BETA1-4 : angle 4.41920 ( 39) link_BETA1-6 : bond 0.00899 ( 6) link_BETA1-6 : angle 2.68395 ( 18) link_NAG-ASN : bond 0.00840 ( 13) link_NAG-ASN : angle 4.29406 ( 39) *********************** 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 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 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: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.6174 (mtt-85) cc_final: 0.5920 (mtt-85) REVERT: A 428 HIS cc_start: 0.6590 (t-90) cc_final: 0.6234 (t-170) REVERT: A 461 ASN cc_start: 0.6920 (t0) cc_final: 0.6571 (t0) REVERT: A 498 THR cc_start: 0.6088 (OUTLIER) cc_final: 0.5647 (t) REVERT: A 584 ASP cc_start: 0.6377 (t0) cc_final: 0.5870 (t0) outliers start: 35 outliers final: 11 residues processed: 152 average time/residue: 0.2989 time to fit residues: 50.7450 Evaluate side-chains 139 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 877 ILE Chi-restraints excluded: chain D residue 910 CYS Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.251346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.235281 restraints weight = 18722.109| |-----------------------------------------------------------------------------| r_work (start): 0.4900 rms_B_bonded: 3.23 r_work: 0.4825 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5034 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8989 Z= 0.133 Angle : 0.805 15.404 12306 Z= 0.352 Chirality : 0.051 0.491 1428 Planarity : 0.004 0.043 1554 Dihedral : 13.789 89.519 1859 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.42 % Favored : 92.39 % Rotamer: Outliers : 2.51 % Allowed : 11.14 % Favored : 86.35 % 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: -0.86 (0.25), residues: 1064 helix: 0.65 (0.69), residues: 59 sheet: 0.21 (0.31), residues: 280 loop : -1.05 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 830 TYR 0.021 0.002 TYR D1004 PHE 0.016 0.002 PHE A 327 TRP 0.025 0.002 TRP D 819 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8939) covalent geometry : angle 0.73380 (12171) SS BOND : bond 0.00335 ( 15) SS BOND : angle 1.03472 ( 30) hydrogen bonds : bond 0.02980 ( 203) hydrogen bonds : angle 5.78507 ( 522) link_ALPHA1-3 : bond 0.01902 ( 2) link_ALPHA1-3 : angle 2.63418 ( 6) link_ALPHA1-6 : bond 0.00986 ( 1) link_ALPHA1-6 : angle 1.25281 ( 3) link_BETA1-4 : bond 0.01020 ( 13) link_BETA1-4 : angle 4.20616 ( 39) link_BETA1-6 : bond 0.00526 ( 6) link_BETA1-6 : angle 2.20925 ( 18) link_NAG-ASN : bond 0.00682 ( 13) link_NAG-ASN : angle 3.81475 ( 39) *********************** 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 158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 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: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.6159 (mtt-85) cc_final: 0.5874 (mtt-85) REVERT: A 356 TRP cc_start: 0.7261 (m100) cc_final: 0.6964 (m-10) REVERT: A 556 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5162 (pp) outliers start: 23 outliers final: 10 residues processed: 148 average time/residue: 0.3429 time to fit residues: 56.6136 Evaluate side-chains 141 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 31 optimal weight: 0.0270 chunk 11 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.250674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.234132 restraints weight = 18736.985| |-----------------------------------------------------------------------------| r_work (start): 0.4897 rms_B_bonded: 3.27 r_work: 0.4824 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8989 Z= 0.144 Angle : 0.826 14.836 12306 Z= 0.365 Chirality : 0.052 0.511 1428 Planarity : 0.004 0.040 1554 Dihedral : 12.123 82.773 1859 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.55 % Favored : 91.26 % Rotamer: Outliers : 3.38 % Allowed : 11.68 % 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 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: -1.06 (0.25), residues: 1064 helix: 0.67 (0.70), residues: 59 sheet: 0.08 (0.31), residues: 286 loop : -1.21 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 830 TYR 0.019 0.002 TYR A 499 PHE 0.016 0.002 PHE A 693 TRP 0.018 0.002 TRP C 144 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8939) covalent geometry : angle 0.75477 (12171) SS BOND : bond 0.00262 ( 15) SS BOND : angle 1.09973 ( 30) hydrogen bonds : bond 0.02955 ( 203) hydrogen bonds : angle 5.92731 ( 522) link_ALPHA1-3 : bond 0.01391 ( 2) link_ALPHA1-3 : angle 2.57513 ( 6) link_ALPHA1-6 : bond 0.00919 ( 1) link_ALPHA1-6 : angle 1.38233 ( 3) link_BETA1-4 : bond 0.00921 ( 13) link_BETA1-4 : angle 4.12066 ( 39) link_BETA1-6 : bond 0.00498 ( 6) link_BETA1-6 : angle 2.15173 ( 18) link_NAG-ASN : bond 0.00773 ( 13) link_NAG-ASN : angle 4.00979 ( 39) *********************** 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 164 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.198 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 258 ARG cc_start: 0.6309 (mtt-85) cc_final: 0.6025 (mtt-85) REVERT: A 356 TRP cc_start: 0.7454 (m100) cc_final: 0.7244 (m-10) REVERT: A 556 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5020 (pp) REVERT: A 622 LEU cc_start: 0.5717 (tt) cc_final: 0.4117 (mm) outliers start: 31 outliers final: 18 residues processed: 151 average time/residue: 0.3401 time to fit residues: 57.3753 Evaluate side-chains 147 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 978 GLN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 762 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 0.0870 chunk 70 optimal weight: 0.0270 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 869 ASN ** C 63 HIS ** 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 = 0.5032 r_free = 0.5032 target = 0.250281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.233720 restraints weight = 18558.677| |-----------------------------------------------------------------------------| r_work (start): 0.4893 rms_B_bonded: 3.28 r_work: 0.4821 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8989 Z= 0.135 Angle : 0.807 15.264 12306 Z= 0.357 Chirality : 0.051 0.502 1428 Planarity : 0.004 0.039 1554 Dihedral : 10.961 76.854 1856 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.80 % Favored : 92.01 % Rotamer: Outliers : 2.51 % Allowed : 13.76 % Favored : 83.73 % 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: -1.10 (0.25), residues: 1064 helix: 0.67 (0.70), residues: 59 sheet: 0.00 (0.30), residues: 291 loop : -1.23 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 830 TYR 0.020 0.001 TYR A 546 PHE 0.021 0.001 PHE A 693 TRP 0.018 0.001 TRP C 144 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8939) covalent geometry : angle 0.73709 (12171) SS BOND : bond 0.00337 ( 15) SS BOND : angle 1.14999 ( 30) hydrogen bonds : bond 0.02858 ( 203) hydrogen bonds : angle 5.93842 ( 522) link_ALPHA1-3 : bond 0.01571 ( 2) link_ALPHA1-3 : angle 2.57896 ( 6) link_ALPHA1-6 : bond 0.00993 ( 1) link_ALPHA1-6 : angle 1.26070 ( 3) link_BETA1-4 : bond 0.00900 ( 13) link_BETA1-4 : angle 4.10841 ( 39) link_BETA1-6 : bond 0.00460 ( 6) link_BETA1-6 : angle 2.02335 ( 18) link_NAG-ASN : bond 0.00691 ( 13) link_NAG-ASN : angle 3.90452 ( 39) *********************** 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 151 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.6322 (mtt-85) cc_final: 0.6026 (mtt-85) REVERT: A 356 TRP cc_start: 0.7505 (m100) cc_final: 0.7171 (m-10) REVERT: A 590 SER cc_start: 0.6794 (m) cc_final: 0.6548 (p) outliers start: 23 outliers final: 19 residues processed: 142 average time/residue: 0.3453 time to fit residues: 54.7405 Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 785 ILE Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 978 GLN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 844 HIS ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** A 445 GLN ** 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 = 0.5020 r_free = 0.5020 target = 0.248692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.232152 restraints weight = 18320.879| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 3.24 r_work: 0.4810 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8989 Z= 0.154 Angle : 0.828 15.481 12306 Z= 0.369 Chirality : 0.052 0.517 1428 Planarity : 0.004 0.037 1554 Dihedral : 10.512 72.316 1856 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.12 % Favored : 90.70 % Rotamer: Outliers : 3.38 % Allowed : 14.30 % 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 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: -1.23 (0.25), residues: 1064 helix: 0.32 (0.66), residues: 65 sheet: -0.10 (0.31), residues: 281 loop : -1.29 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 830 TYR 0.017 0.002 TYR A 546 PHE 0.016 0.001 PHE A 327 TRP 0.019 0.002 TRP D 983 HIS 0.006 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8939) covalent geometry : angle 0.75046 (12171) SS BOND : bond 0.00479 ( 15) SS BOND : angle 1.32025 ( 30) hydrogen bonds : bond 0.02999 ( 203) hydrogen bonds : angle 6.10884 ( 522) link_ALPHA1-3 : bond 0.01526 ( 2) link_ALPHA1-3 : angle 2.77848 ( 6) link_ALPHA1-6 : bond 0.00953 ( 1) link_ALPHA1-6 : angle 1.25351 ( 3) link_BETA1-4 : bond 0.00865 ( 13) link_BETA1-4 : angle 4.10164 ( 39) link_BETA1-6 : bond 0.00432 ( 6) link_BETA1-6 : angle 2.00269 ( 18) link_NAG-ASN : bond 0.00674 ( 13) link_NAG-ASN : angle 4.36358 ( 39) *********************** 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 165 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.330 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: 0.4413 (mmt) cc_final: 0.3687 (pmm) REVERT: A 258 ARG cc_start: 0.6376 (mtt-85) cc_final: 0.6072 (mtt-85) REVERT: A 356 TRP cc_start: 0.7548 (m100) cc_final: 0.7169 (m-10) REVERT: A 556 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5238 (pp) REVERT: A 673 ASP cc_start: 0.4160 (m-30) cc_final: 0.3088 (OUTLIER) outliers start: 31 outliers final: 21 residues processed: 153 average time/residue: 0.3507 time to fit residues: 59.9191 Evaluate side-chains 149 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 785 ILE Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 762 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 0.0060 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 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 = 0.4948 r_free = 0.4948 target = 0.240423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.223206 restraints weight = 17667.999| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 3.30 r_work: 0.4722 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 8989 Z= 0.318 Angle : 1.088 17.552 12306 Z= 0.512 Chirality : 0.060 0.560 1428 Planarity : 0.006 0.065 1554 Dihedral : 12.138 73.955 1856 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.31 % Favored : 87.50 % Rotamer: Outliers : 4.26 % Allowed : 14.08 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.11 (0.24), residues: 1064 helix: -1.15 (0.62), residues: 59 sheet: -0.86 (0.31), residues: 274 loop : -1.73 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 72 TYR 0.025 0.003 TYR A 458 PHE 0.016 0.003 PHE A 479 TRP 0.058 0.004 TRP D 819 HIS 0.018 0.003 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00668 ( 8939) covalent geometry : angle 1.01224 (12171) SS BOND : bond 0.00800 ( 15) SS BOND : angle 1.59577 ( 30) hydrogen bonds : bond 0.05355 ( 203) hydrogen bonds : angle 7.69422 ( 522) link_ALPHA1-3 : bond 0.01111 ( 2) link_ALPHA1-3 : angle 3.57364 ( 6) link_ALPHA1-6 : bond 0.00813 ( 1) link_ALPHA1-6 : angle 1.39694 ( 3) link_BETA1-4 : bond 0.01138 ( 13) link_BETA1-4 : angle 4.61783 ( 39) link_BETA1-6 : bond 0.00917 ( 6) link_BETA1-6 : angle 2.60306 ( 18) link_NAG-ASN : bond 0.00924 ( 13) link_NAG-ASN : angle 5.02323 ( 39) *********************** 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 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.381 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 258 ARG cc_start: 0.6447 (mtt-85) cc_final: 0.6166 (mtt-85) REVERT: A 538 SER cc_start: 0.7500 (p) cc_final: 0.7108 (m) outliers start: 39 outliers final: 19 residues processed: 151 average time/residue: 0.3849 time to fit residues: 64.3114 Evaluate side-chains 145 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 910 CYS Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 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 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.248662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.232295 restraints weight = 18164.657| |-----------------------------------------------------------------------------| r_work (start): 0.4854 rms_B_bonded: 3.22 r_work: 0.4780 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5254 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 0.065 8989 Z= 0.155 Angle : 0.891 15.059 12306 Z= 0.402 Chirality : 0.053 0.540 1428 Planarity : 0.005 0.042 1554 Dihedral : 10.545 64.267 1856 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.12 % Favored : 90.70 % Rotamer: Outliers : 2.73 % Allowed : 16.59 % Favored : 80.68 % 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: -1.79 (0.25), residues: 1064 helix: 0.01 (0.66), residues: 59 sheet: -0.59 (0.32), residues: 269 loop : -1.61 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 830 TYR 0.013 0.002 TYR A 546 PHE 0.024 0.002 PHE A 327 TRP 0.026 0.002 TRP D 819 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8939) covalent geometry : angle 0.81960 (12171) SS BOND : bond 0.00355 ( 15) SS BOND : angle 1.38475 ( 30) hydrogen bonds : bond 0.03167 ( 203) hydrogen bonds : angle 6.86224 ( 522) link_ALPHA1-3 : bond 0.01899 ( 2) link_ALPHA1-3 : angle 3.12476 ( 6) link_ALPHA1-6 : bond 0.00990 ( 1) link_ALPHA1-6 : angle 1.25944 ( 3) link_BETA1-4 : bond 0.00945 ( 13) link_BETA1-4 : angle 4.27410 ( 39) link_BETA1-6 : bond 0.00437 ( 6) link_BETA1-6 : angle 2.00885 ( 18) link_NAG-ASN : bond 0.00672 ( 13) link_NAG-ASN : angle 4.19139 ( 39) *********************** 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 154 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.282 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 258 ARG cc_start: 0.6321 (mtt-85) cc_final: 0.5959 (mtt-85) outliers start: 25 outliers final: 18 residues processed: 142 average time/residue: 0.3154 time to fit residues: 50.2405 Evaluate side-chains 143 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.241727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.225118 restraints weight = 17984.296| |-----------------------------------------------------------------------------| r_work (start): 0.4816 rms_B_bonded: 3.29 r_work: 0.4739 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8989 Z= 0.240 Angle : 0.974 15.797 12306 Z= 0.449 Chirality : 0.056 0.572 1428 Planarity : 0.005 0.043 1554 Dihedral : 10.789 66.799 1856 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.84 % Favored : 87.97 % Rotamer: Outliers : 3.17 % Allowed : 16.38 % Favored : 80.46 % 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: -2.02 (0.24), residues: 1064 helix: -0.58 (0.64), residues: 59 sheet: -0.52 (0.34), residues: 237 loop : -1.80 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 830 TYR 0.023 0.002 TYR A 458 PHE 0.021 0.002 PHE A 327 TRP 0.030 0.003 TRP C 216 HIS 0.012 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8939) covalent geometry : angle 0.90258 (12171) SS BOND : bond 0.00434 ( 15) SS BOND : angle 1.30242 ( 30) hydrogen bonds : bond 0.04069 ( 203) hydrogen bonds : angle 7.30322 ( 522) link_ALPHA1-3 : bond 0.01420 ( 2) link_ALPHA1-3 : angle 3.51349 ( 6) link_ALPHA1-6 : bond 0.00836 ( 1) link_ALPHA1-6 : angle 1.30029 ( 3) link_BETA1-4 : bond 0.01005 ( 13) link_BETA1-4 : angle 4.35932 ( 39) link_BETA1-6 : bond 0.00594 ( 6) link_BETA1-6 : angle 2.17555 ( 18) link_NAG-ASN : bond 0.00801 ( 13) link_NAG-ASN : angle 4.56414 ( 39) *********************** 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 157 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.6460 (mtt-85) cc_final: 0.6149 (mtt-85) REVERT: A 556 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.4983 (pp) REVERT: A 641 GLU cc_start: 0.7984 (tt0) cc_final: 0.7771 (tt0) outliers start: 29 outliers final: 18 residues processed: 144 average time/residue: 0.3303 time to fit residues: 53.1413 Evaluate side-chains 143 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS A 370 GLN ** A 649 GLN ** 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 = 0.4981 r_free = 0.4981 target = 0.244531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.228338 restraints weight = 18055.242| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 3.20 r_work: 0.4774 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8989 Z= 0.159 Angle : 0.904 15.071 12306 Z= 0.413 Chirality : 0.052 0.545 1428 Planarity : 0.005 0.042 1554 Dihedral : 10.201 64.278 1856 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.96 % Favored : 89.85 % 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 : 0.00 % 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: -1.93 (0.24), residues: 1064 helix: -0.00 (0.67), residues: 59 sheet: -0.34 (0.35), residues: 234 loop : -1.83 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 830 TYR 0.018 0.002 TYR A 546 PHE 0.023 0.002 PHE A 327 TRP 0.031 0.002 TRP D 819 HIS 0.005 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8939) covalent geometry : angle 0.83666 (12171) SS BOND : bond 0.00353 ( 15) SS BOND : angle 0.99977 ( 30) hydrogen bonds : bond 0.03151 ( 203) hydrogen bonds : angle 6.85125 ( 522) link_ALPHA1-3 : bond 0.01821 ( 2) link_ALPHA1-3 : angle 3.17608 ( 6) link_ALPHA1-6 : bond 0.00893 ( 1) link_ALPHA1-6 : angle 1.28371 ( 3) link_BETA1-4 : bond 0.00945 ( 13) link_BETA1-4 : angle 4.19515 ( 39) link_BETA1-6 : bond 0.00397 ( 6) link_BETA1-6 : angle 1.92233 ( 18) link_NAG-ASN : bond 0.00703 ( 13) link_NAG-ASN : angle 4.20500 ( 39) ********************** 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 148 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.6424 (mtt-85) cc_final: 0.6076 (mtt-85) REVERT: A 556 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5126 (pp) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.3402 time to fit residues: 52.1745 Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 798 TRP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 96 HIS ** 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 = 0.4952 r_free = 0.4952 target = 0.240968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.224145 restraints weight = 17781.801| |-----------------------------------------------------------------------------| r_work (start): 0.4806 rms_B_bonded: 3.31 r_work: 0.4730 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8989 Z= 0.247 Angle : 0.986 15.860 12306 Z= 0.459 Chirality : 0.056 0.579 1428 Planarity : 0.005 0.059 1554 Dihedral : 10.815 62.446 1856 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.31 % Favored : 87.50 % Rotamer: Outliers : 2.84 % Allowed : 17.36 % 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: -2.21 (0.24), residues: 1064 helix: -0.84 (0.62), residues: 60 sheet: -0.30 (0.36), residues: 208 loop : -2.01 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 830 TYR 0.024 0.002 TYR A 458 PHE 0.023 0.002 PHE A 327 TRP 0.040 0.003 TRP C 216 HIS 0.011 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8939) covalent geometry : angle 0.91456 (12171) SS BOND : bond 0.00438 ( 15) SS BOND : angle 1.39091 ( 30) hydrogen bonds : bond 0.04107 ( 203) hydrogen bonds : angle 7.42007 ( 522) link_ALPHA1-3 : bond 0.01223 ( 2) link_ALPHA1-3 : angle 3.51901 ( 6) link_ALPHA1-6 : bond 0.00848 ( 1) link_ALPHA1-6 : angle 1.33859 ( 3) link_BETA1-4 : bond 0.01006 ( 13) link_BETA1-4 : angle 4.39338 ( 39) link_BETA1-6 : bond 0.00656 ( 6) link_BETA1-6 : angle 2.15491 ( 18) link_NAG-ASN : bond 0.00888 ( 13) link_NAG-ASN : angle 4.58379 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.58 seconds wall clock time: 60 minutes 44.57 seconds (3644.57 seconds total)