Starting phenix.real_space_refine on Sat Jun 7 11:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zj4_60137/06_2025/8zj4_60137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zj4_60137/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zj4_60137/06_2025/8zj4_60137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zj4_60137/06_2025/8zj4_60137.map" model { file = "/net/cci-nas-00/data/ceres_data/8zj4_60137/06_2025/8zj4_60137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zj4_60137/06_2025/8zj4_60137.cif" } resolution = 2.67 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= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.62, per 1000 atoms: 0.64 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: 3.08 Conformation dependent library (CDL) restraints added in 972.1 milliseconds 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: 1.12 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: 2.95 Time building geometry restraints manager: 3.32 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: 0.860 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.230 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- 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 (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: -0.29 (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 TRP 0.005 0.001 TRP C 57 HIS 0.001 0.000 HIS A 647 PHE 0.007 0.001 PHE C 184 TYR 0.006 0.001 TYR A 276 ARG 0.001 0.000 ARG A 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 13) link_NAG-ASN : angle 7.00399 ( 39) 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_ALPHA1-3 : bond 0.00611 ( 2) link_ALPHA1-3 : angle 1.44584 ( 6) hydrogen bonds : bond 0.14815 ( 203) hydrogen bonds : angle 6.45798 ( 522) link_BETA1-6 : bond 0.00463 ( 6) link_BETA1-6 : angle 4.11653 ( 18) SS BOND : bond 0.00096 ( 15) SS BOND : angle 0.60373 ( 30) covalent geometry : bond 0.00472 ( 8939) covalent geometry : angle 0.80815 (12171) *********************** 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 : 0.829 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: 0.6720 time to fit residues: 123.7495 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 : 0.826 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.0770 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 844 HIS D 881 HIS D 981 ASN D1015 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 567 HIS A 575 ASN A 577 ASN A 665 HIS A 768 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.255196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.240495 restraints weight = 19039.680| |-----------------------------------------------------------------------------| r_work (start): 0.4952 rms_B_bonded: 3.08 r_work: 0.4885 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4804 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8989 Z= 0.132 Angle : 0.786 14.455 12306 Z= 0.343 Chirality : 0.050 0.493 1428 Planarity : 0.004 0.043 1554 Dihedral : 16.886 100.412 1862 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.95 % Favored : 92.86 % Rotamer: Outliers : 2.62 % Allowed : 9.28 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1064 helix: 0.71 (0.68), residues: 63 sheet: 0.31 (0.32), residues: 283 loop : -0.74 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 144 HIS 0.005 0.001 HIS A 428 PHE 0.017 0.001 PHE A 327 TYR 0.022 0.002 TYR D1004 ARG 0.006 0.001 ARG D 830 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 13) link_NAG-ASN : angle 3.67627 ( 39) link_ALPHA1-6 : bond 0.00568 ( 1) link_ALPHA1-6 : angle 1.37326 ( 3) link_BETA1-4 : bond 0.00952 ( 13) link_BETA1-4 : angle 3.93923 ( 39) link_ALPHA1-3 : bond 0.01307 ( 2) link_ALPHA1-3 : angle 2.42160 ( 6) hydrogen bonds : bond 0.03324 ( 203) hydrogen bonds : angle 5.66115 ( 522) link_BETA1-6 : bond 0.00549 ( 6) link_BETA1-6 : angle 2.09697 ( 18) SS BOND : bond 0.00315 ( 15) SS BOND : angle 1.06817 ( 30) covalent geometry : bond 0.00283 ( 8939) covalent geometry : angle 0.72067 (12171) *********************** 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 154 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 MET cc_start: 0.5608 (mmt) cc_final: 0.4740 (pmm) REVERT: A 258 ARG cc_start: 0.6072 (mtt-85) cc_final: 0.5848 (mtt-85) REVERT: A 339 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5079 (mt) REVERT: A 348 ASN cc_start: 0.2102 (p0) cc_final: 0.1775 (p0) REVERT: A 356 TRP cc_start: 0.6396 (m100) cc_final: 0.5651 (m100) REVERT: A 546 TYR cc_start: 0.5160 (p90) cc_final: 0.4949 (p90) outliers start: 24 outliers final: 8 residues processed: 145 average time/residue: 0.6695 time to fit residues: 109.0416 Evaluate side-chains 132 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 339 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 578 ASP 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 29 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 40.0000 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 893 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.245391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.228437 restraints weight = 18182.669| |-----------------------------------------------------------------------------| r_work (start): 0.4846 rms_B_bonded: 3.25 r_work: 0.4765 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5269 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8989 Z= 0.270 Angle : 1.021 15.290 12306 Z= 0.468 Chirality : 0.059 0.573 1428 Planarity : 0.006 0.070 1554 Dihedral : 14.689 93.431 1858 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.96 % Favored : 89.85 % Rotamer: Outliers : 3.49 % Allowed : 10.70 % Favored : 85.81 % 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: -1.10 (0.25), residues: 1064 helix: -0.20 (0.65), residues: 65 sheet: 0.23 (0.31), residues: 283 loop : -1.25 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 356 HIS 0.012 0.003 HIS A 384 PHE 0.020 0.002 PHE A 386 TYR 0.021 0.003 TYR D1004 ARG 0.009 0.001 ARG D 807 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 13) link_NAG-ASN : angle 4.43418 ( 39) link_ALPHA1-6 : bond 0.00496 ( 1) link_ALPHA1-6 : angle 1.73007 ( 3) link_BETA1-4 : bond 0.01042 ( 13) link_BETA1-4 : angle 4.39635 ( 39) link_ALPHA1-3 : bond 0.01069 ( 2) link_ALPHA1-3 : angle 2.98454 ( 6) hydrogen bonds : bond 0.04743 ( 203) hydrogen bonds : angle 6.86838 ( 522) link_BETA1-6 : bond 0.00861 ( 6) link_BETA1-6 : angle 2.75732 ( 18) SS BOND : bond 0.00550 ( 15) SS BOND : angle 1.96160 ( 30) covalent geometry : bond 0.00564 ( 8939) covalent geometry : angle 0.95069 (12171) *********************** 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 164 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.813 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: D 1007 VAL cc_start: 0.7145 (m) cc_final: 0.6938 (p) REVERT: A 258 ARG cc_start: 0.6290 (mtt-85) cc_final: 0.6029 (mtt-85) REVERT: A 538 SER cc_start: 0.7227 (p) cc_final: 0.7018 (m) REVERT: A 700 HIS cc_start: 0.5108 (OUTLIER) cc_final: 0.4874 (p90) outliers start: 32 outliers final: 18 residues processed: 151 average time/residue: 0.6812 time to fit residues: 114.9079 Evaluate side-chains 146 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 821 VAL Chi-restraints excluded: chain D residue 877 ILE Chi-restraints excluded: chain D residue 891 TYR Chi-restraints excluded: chain D residue 910 CYS Chi-restraints excluded: chain D residue 949 ASN Chi-restraints excluded: chain D residue 956 CYS 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 470 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 700 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.248647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.232291 restraints weight = 18420.787| |-----------------------------------------------------------------------------| r_work (start): 0.4877 rms_B_bonded: 3.20 r_work: 0.4803 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 moved from start: 0.3483 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= 0.146 Angle : 0.833 15.585 12306 Z= 0.364 Chirality : 0.052 0.515 1428 Planarity : 0.004 0.038 1554 Dihedral : 12.750 86.046 1856 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.61 % Favored : 92.20 % Rotamer: Outliers : 3.06 % Allowed : 12.34 % Favored : 84.61 % 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: -1.10 (0.25), residues: 1064 helix: 0.19 (0.65), residues: 65 sheet: 0.16 (0.32), residues: 273 loop : -1.24 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 819 HIS 0.003 0.001 HIS A 384 PHE 0.014 0.002 PHE A 327 TYR 0.020 0.001 TYR A 499 ARG 0.007 0.001 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00835 ( 13) link_NAG-ASN : angle 4.00281 ( 39) link_ALPHA1-6 : bond 0.00965 ( 1) link_ALPHA1-6 : angle 1.39035 ( 3) link_BETA1-4 : bond 0.00964 ( 13) link_BETA1-4 : angle 4.23456 ( 39) link_ALPHA1-3 : bond 0.01587 ( 2) link_ALPHA1-3 : angle 2.62251 ( 6) hydrogen bonds : bond 0.03147 ( 203) hydrogen bonds : angle 6.18712 ( 522) link_BETA1-6 : bond 0.00533 ( 6) link_BETA1-6 : angle 2.27367 ( 18) SS BOND : bond 0.00455 ( 15) SS BOND : angle 1.19647 ( 30) covalent geometry : bond 0.00313 ( 8939) covalent geometry : angle 0.75982 (12171) *********************** 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 160 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.844 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: 0.6237 (mtt-85) cc_final: 0.5885 (mtt-85) REVERT: A 356 TRP cc_start: 0.7599 (m100) cc_final: 0.7328 (m-10) outliers start: 28 outliers final: 16 residues processed: 145 average time/residue: 0.6761 time to fit residues: 109.7519 Evaluate side-chains 146 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 D residue 910 CYS Chi-restraints excluded: chain D residue 933 VAL Chi-restraints excluded: chain D residue 978 GLN 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 556 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 GLN 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 102 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 0.0050 chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 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 = 0.5030 r_free = 0.5030 target = 0.250127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.233742 restraints weight = 18479.379| |-----------------------------------------------------------------------------| r_work (start): 0.4894 rms_B_bonded: 3.22 r_work: 0.4825 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5069 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8989 Z= 0.130 Angle : 0.811 15.271 12306 Z= 0.357 Chirality : 0.051 0.522 1428 Planarity : 0.004 0.037 1554 Dihedral : 11.135 78.256 1856 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 2.84 % Allowed : 13.65 % Favored : 83.52 % 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: -1.15 (0.25), residues: 1064 helix: 0.36 (0.66), residues: 65 sheet: -0.03 (0.32), residues: 261 loop : -1.21 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 819 HIS 0.009 0.001 HIS A 700 PHE 0.015 0.001 PHE A 327 TYR 0.020 0.001 TYR A 546 ARG 0.007 0.000 ARG D 830 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 13) link_NAG-ASN : angle 4.04329 ( 39) link_ALPHA1-6 : bond 0.01042 ( 1) link_ALPHA1-6 : angle 1.32469 ( 3) link_BETA1-4 : bond 0.00971 ( 13) link_BETA1-4 : angle 4.12231 ( 39) link_ALPHA1-3 : bond 0.01782 ( 2) link_ALPHA1-3 : angle 2.62848 ( 6) hydrogen bonds : bond 0.02673 ( 203) hydrogen bonds : angle 5.99859 ( 522) link_BETA1-6 : bond 0.00536 ( 6) link_BETA1-6 : angle 2.07791 ( 18) SS BOND : bond 0.00404 ( 15) SS BOND : angle 1.24767 ( 30) covalent geometry : bond 0.00284 ( 8939) covalent geometry : angle 0.73795 (12171) *********************** 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 157 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.901 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: 0.6302 (mtt-85) cc_final: 0.5945 (mtt-85) REVERT: A 356 TRP cc_start: 0.7449 (m100) cc_final: 0.7022 (m-10) REVERT: A 357 VAL cc_start: 0.7617 (t) cc_final: 0.7350 (p) REVERT: A 612 MET cc_start: 0.2980 (tpp) cc_final: 0.2651 (tpp) REVERT: A 622 LEU cc_start: 0.5599 (tt) cc_final: 0.5117 (tt) outliers start: 26 outliers final: 13 residues processed: 144 average time/residue: 0.6926 time to fit residues: 111.2272 Evaluate side-chains 139 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 574 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.249393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.233111 restraints weight = 18020.227| |-----------------------------------------------------------------------------| r_work (start): 0.4890 rms_B_bonded: 3.15 r_work: 0.4817 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5096 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8989 Z= 0.139 Angle : 0.836 15.165 12306 Z= 0.367 Chirality : 0.053 0.542 1428 Planarity : 0.004 0.038 1554 Dihedral : 11.032 83.898 1856 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.82 % Rotamer: Outliers : 3.06 % Allowed : 14.19 % Favored : 82.75 % 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: -1.24 (0.25), residues: 1064 helix: 0.35 (0.66), residues: 65 sheet: -0.11 (0.30), residues: 290 loop : -1.31 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 144 HIS 0.007 0.001 HIS A 700 PHE 0.017 0.001 PHE A 479 TYR 0.018 0.001 TYR A 546 ARG 0.007 0.000 ARG D 830 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 13) link_NAG-ASN : angle 4.46148 ( 39) link_ALPHA1-6 : bond 0.00975 ( 1) link_ALPHA1-6 : angle 1.26510 ( 3) link_BETA1-4 : bond 0.01006 ( 13) link_BETA1-4 : angle 4.32126 ( 39) link_ALPHA1-3 : bond 0.01716 ( 2) link_ALPHA1-3 : angle 2.84052 ( 6) hydrogen bonds : bond 0.02810 ( 203) hydrogen bonds : angle 6.03001 ( 522) link_BETA1-6 : bond 0.00720 ( 6) link_BETA1-6 : angle 2.28954 ( 18) SS BOND : bond 0.00362 ( 15) SS BOND : angle 1.14953 ( 30) covalent geometry : bond 0.00298 ( 8939) covalent geometry : angle 0.75375 (12171) *********************** 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 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.6301 (mtt-85) cc_final: 0.5928 (mtt-85) REVERT: A 356 TRP cc_start: 0.7476 (m100) cc_final: 0.7272 (m-10) REVERT: A 357 VAL cc_start: 0.7616 (t) cc_final: 0.7365 (p) outliers start: 28 outliers final: 17 residues processed: 143 average time/residue: 0.6960 time to fit residues: 111.4986 Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 C residue 225 LYS 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 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 Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 717 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 chunk 37 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS A 433 ASN A 461 ASN ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.247681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.231230 restraints weight = 18166.273| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 3.25 r_work: 0.4777 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.4464 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= 0.214 Angle : 0.929 16.038 12306 Z= 0.419 Chirality : 0.054 0.582 1428 Planarity : 0.004 0.036 1554 Dihedral : 11.281 87.952 1856 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.34 % Favored : 89.47 % Rotamer: Outliers : 2.84 % Allowed : 14.96 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1064 helix: 0.01 (0.64), residues: 65 sheet: -0.61 (0.31), residues: 277 loop : -1.45 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 819 HIS 0.012 0.002 HIS A 384 PHE 0.018 0.002 PHE A 479 TYR 0.021 0.002 TYR A 546 ARG 0.009 0.001 ARG A 368 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 13) link_NAG-ASN : angle 4.53088 ( 39) link_ALPHA1-6 : bond 0.00865 ( 1) link_ALPHA1-6 : angle 1.32625 ( 3) link_BETA1-4 : bond 0.01068 ( 13) link_BETA1-4 : angle 4.52462 ( 39) link_ALPHA1-3 : bond 0.01438 ( 2) link_ALPHA1-3 : angle 3.29039 ( 6) hydrogen bonds : bond 0.03744 ( 203) hydrogen bonds : angle 6.68521 ( 522) link_BETA1-6 : bond 0.00647 ( 6) link_BETA1-6 : angle 2.28760 ( 18) SS BOND : bond 0.00385 ( 15) SS BOND : angle 1.24154 ( 30) covalent geometry : bond 0.00454 ( 8939) covalent geometry : angle 0.85082 (12171) *********************** 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 160 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.833 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: 0.6406 (mtt-85) cc_final: 0.6087 (mtt-85) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.7289 time to fit residues: 121.2173 Evaluate side-chains 145 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 989 THR Chi-restraints excluded: chain C residue 225 LYS 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 556 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 739 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3622 > 50: distance: 13 - 19: 7.305 distance: 14 - 48: 21.540 distance: 19 - 20: 14.525 distance: 20 - 21: 5.495 distance: 20 - 23: 22.770 distance: 21 - 22: 21.045 distance: 21 - 27: 26.861 distance: 23 - 24: 17.105 distance: 24 - 25: 7.371 distance: 24 - 26: 10.677 distance: 27 - 28: 10.836 distance: 28 - 29: 32.219 distance: 28 - 31: 23.797 distance: 29 - 30: 11.013 distance: 29 - 39: 7.740 distance: 30 - 65: 11.462 distance: 31 - 32: 18.374 distance: 32 - 33: 25.733 distance: 32 - 34: 29.096 distance: 33 - 35: 15.735 distance: 35 - 37: 33.565 distance: 36 - 37: 13.203 distance: 37 - 38: 10.730 distance: 39 - 40: 10.750 distance: 40 - 41: 8.531 distance: 40 - 43: 13.995 distance: 41 - 42: 14.786 distance: 41 - 48: 8.134 distance: 43 - 44: 9.904 distance: 44 - 45: 27.541 distance: 45 - 46: 8.818 distance: 45 - 47: 5.942 distance: 48 - 49: 6.459 distance: 49 - 50: 10.566 distance: 49 - 52: 17.353 distance: 50 - 51: 18.723 distance: 50 - 57: 5.267 distance: 52 - 53: 7.464 distance: 53 - 54: 12.338 distance: 54 - 55: 19.151 distance: 55 - 56: 12.284 distance: 57 - 58: 6.784 distance: 58 - 59: 4.522 distance: 58 - 61: 7.890 distance: 59 - 60: 11.652 distance: 59 - 65: 10.240 distance: 61 - 62: 12.272 distance: 61 - 63: 10.279 distance: 62 - 64: 7.247 distance: 66 - 67: 5.249 distance: 66 - 69: 8.992 distance: 67 - 73: 7.585 distance: 69 - 70: 4.797 distance: 70 - 71: 10.097 distance: 70 - 72: 18.045 distance: 73 - 74: 6.989 distance: 74 - 75: 8.485 distance: 74 - 77: 9.033 distance: 75 - 76: 6.901 distance: 75 - 79: 7.889 distance: 77 - 78: 11.051 distance: 78 - 128: 10.129 distance: 79 - 80: 5.956 distance: 80 - 81: 3.066 distance: 80 - 83: 6.994 distance: 81 - 82: 6.342 distance: 81 - 87: 9.756 distance: 83 - 84: 10.150 distance: 84 - 85: 4.656 distance: 84 - 86: 15.769 distance: 88 - 91: 3.375 distance: 89 - 90: 4.693 distance: 91 - 92: 6.989 distance: 92 - 93: 7.996 distance: 92 - 94: 5.871 distance: 93 - 95: 5.906 distance: 94 - 96: 9.442 distance: 95 - 97: 12.274 distance: 96 - 97: 8.162 distance: 98 - 99: 5.940 distance: 99 - 100: 5.654 distance: 99 - 102: 5.397 distance: 100 - 101: 3.460 distance: 102 - 103: 3.435 distance: 103 - 104: 5.015 distance: 104 - 105: 8.359 distance: 104 - 106: 8.718