Starting phenix.real_space_refine on Sat Aug 23 03:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vq9_43435/08_2025/8vq9_43435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vq9_43435/08_2025/8vq9_43435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vq9_43435/08_2025/8vq9_43435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vq9_43435/08_2025/8vq9_43435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vq9_43435/08_2025/8vq9_43435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vq9_43435/08_2025/8vq9_43435.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.105 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 63 5.16 5 C 6090 2.51 5 N 1614 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9513 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 11, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 11, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 11, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "D" 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: "E" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "I" 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: "J" 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: "K" 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: "L" 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.69, per 1000 atoms: 0.28 Number of scatterers: 9513 At special positions: 0 Unit cell: (88, 91, 136, 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 63 16.00 O 1746 8.00 N 1614 7.00 C 6090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS C 883 " distance=2.20 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.10 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 707 " distance=2.20 Simple disulfide: pdb=" SG CYS A 970 " - pdb=" SG CYS A 999 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.10 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS C 707 " distance=2.20 Simple disulfide: pdb=" SG CYS B 970 " - pdb=" SG CYS B 999 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.10 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 970 " - pdb=" SG CYS C 999 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 379.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 50.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.115A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.114A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.114A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.395A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1122 567 hydrogen bonds defined for protein. 1647 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: 1.62 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2535 1.33 - 1.45: 1860 1.45 - 1.58: 5217 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 9696 Sorted by residual: bond pdb=" C5 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.19e+00 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11722 1.64 - 3.27: 1275 3.27 - 4.91: 128 4.91 - 6.55: 90 6.55 - 8.19: 33 Bond angle restraints: 13248 Sorted by residual: angle pdb=" C ALA C1078 " pdb=" N PRO C1079 " pdb=" CA PRO C1079 " ideal model delta sigma weight residual 119.24 127.43 -8.19 1.04e+00 9.25e-01 6.20e+01 angle pdb=" C ALA B1078 " pdb=" N PRO B1079 " pdb=" CA PRO B1079 " ideal model delta sigma weight residual 119.24 127.38 -8.14 1.04e+00 9.25e-01 6.12e+01 angle pdb=" C ALA A1078 " pdb=" N PRO A1079 " pdb=" CA PRO A1079 " ideal model delta sigma weight residual 119.24 127.38 -8.14 1.04e+00 9.25e-01 6.12e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.68 -7.65 9.90e-01 1.02e+00 5.97e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.66 -7.63 9.90e-01 1.02e+00 5.95e+01 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5868 17.95 - 35.91: 201 35.91 - 53.86: 39 53.86 - 71.82: 6 71.82 - 89.77: 9 Dihedral angle restraints: 6123 sinusoidal: 2418 harmonic: 3705 Sorted by residual: dihedral pdb=" CB CYS B 883 " pdb=" SG CYS B 883 " pdb=" SG CYS C 707 " pdb=" CB CYS C 707 " ideal model delta sinusoidal sigma weight residual -86.00 -37.56 -48.44 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS B 707 " pdb=" CB CYS B 707 " ideal model delta sinusoidal sigma weight residual -86.00 -37.57 -48.43 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 707 " pdb=" SG CYS A 707 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual -86.00 -37.59 -48.41 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 6120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1230 0.078 - 0.156: 318 0.156 - 0.234: 63 0.234 - 0.312: 27 0.312 - 0.390: 12 Chirality restraints: 1650 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.27e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.26e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.24e+01 ... (remaining 1647 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.052 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.051 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR C 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " -0.051 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " -0.040 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4997 2.99 - 3.47: 9255 3.47 - 3.94: 15145 3.94 - 4.42: 17532 4.42 - 4.90: 27446 Nonbonded interactions: 74375 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS C1028 " pdb=" O PHE C1042 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.511 3.120 nonbonded pdb=" OE1 GLN B1011 " pdb=" NH1 ARG B1014 " model vdw 2.582 3.120 nonbonded pdb=" OE1 GLN A1011 " pdb=" NH1 ARG A1014 " model vdw 2.582 3.120 ... (remaining 74370 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.120 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.011 0.171 9744 Z= 0.626 Angle : 1.223 8.186 13371 Z= 0.814 Chirality : 0.082 0.390 1650 Planarity : 0.004 0.028 1698 Dihedral : 9.901 89.774 3654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.54 (0.21), residues: 1248 helix: 1.19 (0.20), residues: 570 sheet: 1.57 (0.43), residues: 120 loop : -0.78 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.052 0.005 TYR B 904 PHE 0.017 0.003 PHE C 833 TRP 0.016 0.006 TRP C 886 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01044 ( 9696) covalent geometry : angle 1.19681 (13248) SS BOND : bond 0.07067 ( 21) SS BOND : angle 3.35327 ( 42) hydrogen bonds : bond 0.20761 ( 567) hydrogen bonds : angle 7.24409 ( 1647) link_BETA1-4 : bond 0.05208 ( 9) link_BETA1-4 : angle 3.08948 ( 27) link_NAG-ASN : bond 0.05500 ( 18) link_NAG-ASN : angle 2.38757 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.260 Fit side-chains REVERT: A 725 GLU cc_start: 0.7970 (tt0) cc_final: 0.7712 (tt0) REVERT: A 855 PHE cc_start: 0.7618 (m-80) cc_final: 0.7404 (m-80) REVERT: A 935 GLN cc_start: 0.7494 (mt0) cc_final: 0.7268 (mt0) REVERT: B 1029 MET cc_start: 0.8402 (tpp) cc_final: 0.8088 (tpp) REVERT: C 725 GLU cc_start: 0.8028 (tt0) cc_final: 0.7764 (tt0) REVERT: C 752 LEU cc_start: 0.8316 (mt) cc_final: 0.8089 (mt) REVERT: C 803 SER cc_start: 0.8512 (p) cc_final: 0.8217 (p) REVERT: C 1138 TYR cc_start: 0.7781 (t80) cc_final: 0.7420 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.6082 time to fit residues: 113.8122 Evaluate side-chains 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 907 ASN A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 755 GLN B 907 ASN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 907 ASN C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118784 restraints weight = 9571.554| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.82 r_work: 0.3181 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9744 Z= 0.164 Angle : 0.616 8.549 13371 Z= 0.318 Chirality : 0.042 0.135 1650 Planarity : 0.005 0.042 1698 Dihedral : 4.121 16.065 1893 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.50 % Allowed : 9.40 % 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 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: 1.71 (0.23), residues: 1248 helix: 2.61 (0.21), residues: 570 sheet: 1.21 (0.38), residues: 153 loop : -0.59 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1019 TYR 0.018 0.002 TYR C1067 PHE 0.019 0.002 PHE C 906 TRP 0.010 0.002 TRP A 886 HIS 0.003 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9696) covalent geometry : angle 0.59089 (13248) SS BOND : bond 0.00462 ( 21) SS BOND : angle 1.61565 ( 42) hydrogen bonds : bond 0.06828 ( 567) hydrogen bonds : angle 5.05374 ( 1647) link_BETA1-4 : bond 0.00814 ( 9) link_BETA1-4 : angle 2.11371 ( 27) link_NAG-ASN : bond 0.00656 ( 18) link_NAG-ASN : angle 1.97250 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.377 Fit side-chains REVERT: A 725 GLU cc_start: 0.8453 (tt0) cc_final: 0.8112 (tt0) REVERT: A 752 LEU cc_start: 0.8646 (mt) cc_final: 0.8325 (mt) REVERT: A 855 PHE cc_start: 0.7699 (m-80) cc_final: 0.7410 (m-80) REVERT: A 935 GLN cc_start: 0.7101 (mt0) cc_final: 0.6734 (mt0) REVERT: B 804 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: B 904 TYR cc_start: 0.7975 (m-10) cc_final: 0.7061 (m-10) REVERT: C 725 GLU cc_start: 0.8457 (tt0) cc_final: 0.8111 (tt0) REVERT: C 752 LEU cc_start: 0.8569 (mt) cc_final: 0.8359 (mt) outliers start: 21 outliers final: 5 residues processed: 128 average time/residue: 0.6315 time to fit residues: 86.2134 Evaluate side-chains 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 chunk 94 optimal weight: 0.3980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113362 restraints weight = 9467.179| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.76 r_work: 0.3109 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9744 Z= 0.165 Angle : 0.567 5.104 13371 Z= 0.296 Chirality : 0.042 0.132 1650 Planarity : 0.005 0.043 1698 Dihedral : 3.716 16.369 1893 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.14 % Allowed : 10.00 % Favored : 87.86 % 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: 1.66 (0.23), residues: 1248 helix: 2.60 (0.21), residues: 585 sheet: 1.07 (0.37), residues: 153 loop : -0.72 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1014 TYR 0.020 0.002 TYR C1067 PHE 0.021 0.002 PHE C 906 TRP 0.014 0.003 TRP A 886 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9696) covalent geometry : angle 0.54567 (13248) SS BOND : bond 0.00527 ( 21) SS BOND : angle 1.56627 ( 42) hydrogen bonds : bond 0.06330 ( 567) hydrogen bonds : angle 4.83453 ( 1647) link_BETA1-4 : bond 0.00835 ( 9) link_BETA1-4 : angle 1.62099 ( 27) link_NAG-ASN : bond 0.00462 ( 18) link_NAG-ASN : angle 1.81857 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.432 Fit side-chains REVERT: A 725 GLU cc_start: 0.8510 (tt0) cc_final: 0.8156 (tt0) REVERT: A 731 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8630 (ptt) REVERT: A 752 LEU cc_start: 0.8681 (mt) cc_final: 0.8390 (mt) REVERT: A 815 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7812 (mtm-85) REVERT: A 855 PHE cc_start: 0.7806 (m-80) cc_final: 0.7463 (m-80) REVERT: A 935 GLN cc_start: 0.6989 (mt0) cc_final: 0.6488 (mt0) REVERT: B 731 MET cc_start: 0.8794 (ptt) cc_final: 0.8444 (ptp) REVERT: B 904 TYR cc_start: 0.7911 (m-10) cc_final: 0.7155 (m-10) REVERT: B 1119 ASN cc_start: 0.7783 (m-40) cc_final: 0.7485 (m110) REVERT: C 725 GLU cc_start: 0.8530 (tt0) cc_final: 0.8198 (tt0) REVERT: C 752 LEU cc_start: 0.8616 (mt) cc_final: 0.8387 (mt) REVERT: C 900 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: C 904 TYR cc_start: 0.8050 (m-10) cc_final: 0.7798 (m-10) REVERT: C 935 GLN cc_start: 0.7247 (mt0) cc_final: 0.7023 (mt0) outliers start: 18 outliers final: 5 residues processed: 123 average time/residue: 0.6490 time to fit residues: 85.0161 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.0670 chunk 17 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN C 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113150 restraints weight = 9601.305| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.76 r_work: 0.3074 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9744 Z= 0.176 Angle : 0.580 5.128 13371 Z= 0.299 Chirality : 0.042 0.138 1650 Planarity : 0.005 0.041 1698 Dihedral : 3.878 16.147 1893 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.67 % Allowed : 10.71 % Favored : 87.62 % 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: 1.47 (0.23), residues: 1248 helix: 2.44 (0.21), residues: 597 sheet: 0.90 (0.37), residues: 153 loop : -0.89 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1014 TYR 0.019 0.002 TYR C1067 PHE 0.016 0.002 PHE C 906 TRP 0.017 0.003 TRP C 886 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9696) covalent geometry : angle 0.55989 (13248) SS BOND : bond 0.00399 ( 21) SS BOND : angle 1.50017 ( 42) hydrogen bonds : bond 0.06215 ( 567) hydrogen bonds : angle 4.82195 ( 1647) link_BETA1-4 : bond 0.00508 ( 9) link_BETA1-4 : angle 1.46289 ( 27) link_NAG-ASN : bond 0.00356 ( 18) link_NAG-ASN : angle 1.85707 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.377 Fit side-chains REVERT: A 725 GLU cc_start: 0.8543 (tt0) cc_final: 0.8167 (tt0) REVERT: A 815 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7710 (mtm-85) REVERT: A 855 PHE cc_start: 0.7945 (m-80) cc_final: 0.7552 (m-80) REVERT: B 904 TYR cc_start: 0.7846 (m-10) cc_final: 0.7117 (m-10) REVERT: C 725 GLU cc_start: 0.8559 (tt0) cc_final: 0.8252 (tt0) REVERT: C 752 LEU cc_start: 0.8650 (mt) cc_final: 0.8399 (mt) REVERT: C 815 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: C 904 TYR cc_start: 0.8096 (m-10) cc_final: 0.7810 (m-10) REVERT: C 1119 ASN cc_start: 0.8008 (m-40) cc_final: 0.7698 (m110) outliers start: 14 outliers final: 7 residues processed: 115 average time/residue: 0.6865 time to fit residues: 83.9056 Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111530 restraints weight = 9630.615| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.76 r_work: 0.3066 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9744 Z= 0.205 Angle : 0.612 9.363 13371 Z= 0.314 Chirality : 0.043 0.140 1650 Planarity : 0.005 0.043 1698 Dihedral : 4.119 17.518 1893 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.02 % Allowed : 11.90 % Favored : 86.07 % 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: 1.25 (0.23), residues: 1248 helix: 2.28 (0.21), residues: 600 sheet: 0.61 (0.37), residues: 159 loop : -0.98 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1014 TYR 0.021 0.002 TYR C1067 PHE 0.015 0.002 PHE B 906 TRP 0.013 0.003 TRP C 886 HIS 0.004 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9696) covalent geometry : angle 0.59325 (13248) SS BOND : bond 0.00400 ( 21) SS BOND : angle 1.50247 ( 42) hydrogen bonds : bond 0.06577 ( 567) hydrogen bonds : angle 4.90214 ( 1647) link_BETA1-4 : bond 0.00541 ( 9) link_BETA1-4 : angle 1.37681 ( 27) link_NAG-ASN : bond 0.00338 ( 18) link_NAG-ASN : angle 1.89529 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.375 Fit side-chains REVERT: A 725 GLU cc_start: 0.8566 (tt0) cc_final: 0.8250 (tt0) REVERT: A 731 MET cc_start: 0.8940 (ptt) cc_final: 0.8739 (ptt) REVERT: A 855 PHE cc_start: 0.7978 (m-80) cc_final: 0.7641 (m-80) REVERT: B 731 MET cc_start: 0.8905 (ptt) cc_final: 0.8459 (ptp) REVERT: B 904 TYR cc_start: 0.7849 (m-10) cc_final: 0.7091 (m-10) REVERT: B 969 ASN cc_start: 0.8594 (m-40) cc_final: 0.8370 (m110) REVERT: C 725 GLU cc_start: 0.8556 (tt0) cc_final: 0.8296 (tt0) REVERT: C 752 LEU cc_start: 0.8618 (mt) cc_final: 0.8369 (mt) REVERT: C 815 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: C 904 TYR cc_start: 0.8101 (m-10) cc_final: 0.7793 (m-10) outliers start: 17 outliers final: 7 residues processed: 108 average time/residue: 0.6984 time to fit residues: 80.0921 Evaluate side-chains 108 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 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 = 0.3638 r_free = 0.3638 target = 0.146557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114317 restraints weight = 9587.707| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.75 r_work: 0.3095 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9744 Z= 0.138 Angle : 0.526 8.114 13371 Z= 0.271 Chirality : 0.040 0.126 1650 Planarity : 0.004 0.040 1698 Dihedral : 3.837 15.698 1893 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 12.86 % Favored : 85.71 % 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: 1.52 (0.23), residues: 1248 helix: 2.54 (0.21), residues: 597 sheet: 0.95 (0.37), residues: 153 loop : -0.95 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.016 0.002 TYR C1067 PHE 0.012 0.001 PHE B1121 TRP 0.009 0.002 TRP C 886 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9696) covalent geometry : angle 0.51015 (13248) SS BOND : bond 0.00332 ( 21) SS BOND : angle 1.33818 ( 42) hydrogen bonds : bond 0.05573 ( 567) hydrogen bonds : angle 4.71382 ( 1647) link_BETA1-4 : bond 0.00510 ( 9) link_BETA1-4 : angle 1.21209 ( 27) link_NAG-ASN : bond 0.00306 ( 18) link_NAG-ASN : angle 1.61694 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.365 Fit side-chains REVERT: A 725 GLU cc_start: 0.8557 (tt0) cc_final: 0.8190 (tt0) REVERT: A 731 MET cc_start: 0.8925 (ptt) cc_final: 0.8699 (ptt) REVERT: A 751 ASN cc_start: 0.7857 (m-40) cc_final: 0.7356 (m-40) REVERT: A 1119 ASN cc_start: 0.8052 (m-40) cc_final: 0.7813 (m110) REVERT: B 731 MET cc_start: 0.8854 (ptt) cc_final: 0.8472 (ptp) REVERT: B 904 TYR cc_start: 0.7796 (m-10) cc_final: 0.7075 (m-10) REVERT: C 725 GLU cc_start: 0.8561 (tt0) cc_final: 0.8315 (tt0) REVERT: C 752 LEU cc_start: 0.8623 (mt) cc_final: 0.8399 (mt) REVERT: C 755 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: C 904 TYR cc_start: 0.8120 (m-10) cc_final: 0.7809 (m-10) REVERT: C 1119 ASN cc_start: 0.7976 (m-40) cc_final: 0.7679 (m110) outliers start: 12 outliers final: 4 residues processed: 109 average time/residue: 0.6809 time to fit residues: 78.8407 Evaluate side-chains 105 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 0.0470 chunk 110 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114991 restraints weight = 9700.308| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.75 r_work: 0.3098 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9744 Z= 0.123 Angle : 0.504 8.215 13371 Z= 0.259 Chirality : 0.040 0.126 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.707 16.586 1893 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 13.10 % Favored : 85.12 % 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: 1.66 (0.23), residues: 1248 helix: 2.66 (0.21), residues: 597 sheet: 0.99 (0.37), residues: 153 loop : -0.88 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.016 0.001 TYR C1067 PHE 0.011 0.001 PHE B1121 TRP 0.007 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9696) covalent geometry : angle 0.48880 (13248) SS BOND : bond 0.00309 ( 21) SS BOND : angle 1.30452 ( 42) hydrogen bonds : bond 0.05174 ( 567) hydrogen bonds : angle 4.59901 ( 1647) link_BETA1-4 : bond 0.00472 ( 9) link_BETA1-4 : angle 1.11072 ( 27) link_NAG-ASN : bond 0.00269 ( 18) link_NAG-ASN : angle 1.50553 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.379 Fit side-chains REVERT: A 725 GLU cc_start: 0.8537 (tt0) cc_final: 0.8174 (tt0) REVERT: A 1119 ASN cc_start: 0.7977 (m-40) cc_final: 0.7747 (m110) REVERT: B 731 MET cc_start: 0.8853 (ptt) cc_final: 0.8485 (ptp) REVERT: B 904 TYR cc_start: 0.7787 (m-10) cc_final: 0.7064 (m-10) REVERT: B 1119 ASN cc_start: 0.7978 (m-40) cc_final: 0.7669 (m110) REVERT: C 725 GLU cc_start: 0.8550 (tt0) cc_final: 0.8342 (tt0) REVERT: C 752 LEU cc_start: 0.8650 (mt) cc_final: 0.8421 (mt) REVERT: C 765 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7672 (mtp85) REVERT: C 815 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7428 (mtp180) REVERT: C 904 TYR cc_start: 0.8013 (m-10) cc_final: 0.7803 (m-10) outliers start: 15 outliers final: 3 residues processed: 112 average time/residue: 0.6534 time to fit residues: 77.8883 Evaluate side-chains 105 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 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 = 0.3629 r_free = 0.3629 target = 0.145546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113354 restraints weight = 9603.650| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.74 r_work: 0.3091 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9744 Z= 0.195 Angle : 0.590 7.578 13371 Z= 0.303 Chirality : 0.043 0.129 1650 Planarity : 0.004 0.041 1698 Dihedral : 4.056 17.648 1893 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.38 % Allowed : 12.62 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.45 (0.23), residues: 1248 helix: 2.53 (0.22), residues: 579 sheet: 0.66 (0.37), residues: 159 loop : -0.84 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1039 TYR 0.020 0.002 TYR C1067 PHE 0.012 0.002 PHE C 898 TRP 0.009 0.002 TRP B 886 HIS 0.004 0.002 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9696) covalent geometry : angle 0.57273 (13248) SS BOND : bond 0.00372 ( 21) SS BOND : angle 1.46254 ( 42) hydrogen bonds : bond 0.06234 ( 567) hydrogen bonds : angle 4.80358 ( 1647) link_BETA1-4 : bond 0.00496 ( 9) link_BETA1-4 : angle 1.22715 ( 27) link_NAG-ASN : bond 0.00270 ( 18) link_NAG-ASN : angle 1.78138 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.319 Fit side-chains REVERT: A 725 GLU cc_start: 0.8570 (tt0) cc_final: 0.8208 (tt0) REVERT: B 731 MET cc_start: 0.8903 (ptt) cc_final: 0.8448 (ptp) REVERT: B 904 TYR cc_start: 0.7839 (m-10) cc_final: 0.7115 (m-10) REVERT: C 725 GLU cc_start: 0.8592 (tt0) cc_final: 0.8324 (tt0) REVERT: C 755 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: C 1119 ASN cc_start: 0.8030 (m-40) cc_final: 0.7744 (m110) outliers start: 20 outliers final: 5 residues processed: 113 average time/residue: 0.6213 time to fit residues: 74.6395 Evaluate side-chains 107 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 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 = 0.3631 r_free = 0.3631 target = 0.146166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113704 restraints weight = 9642.232| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.76 r_work: 0.3094 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9744 Z= 0.137 Angle : 0.525 7.649 13371 Z= 0.271 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.840 18.914 1893 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.19 % Allowed : 14.29 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.64 (0.23), residues: 1248 helix: 2.69 (0.22), residues: 579 sheet: 0.98 (0.37), residues: 153 loop : -0.82 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.016 0.002 TYR C1067 PHE 0.011 0.001 PHE B1121 TRP 0.008 0.002 TRP B 886 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9696) covalent geometry : angle 0.51013 (13248) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.33567 ( 42) hydrogen bonds : bond 0.05384 ( 567) hydrogen bonds : angle 4.66306 ( 1647) link_BETA1-4 : bond 0.00489 ( 9) link_BETA1-4 : angle 1.10597 ( 27) link_NAG-ASN : bond 0.00250 ( 18) link_NAG-ASN : angle 1.56107 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.314 Fit side-chains REVERT: A 725 GLU cc_start: 0.8557 (tt0) cc_final: 0.8189 (tt0) REVERT: A 1119 ASN cc_start: 0.8032 (m-40) cc_final: 0.7790 (m110) REVERT: B 731 MET cc_start: 0.8892 (ptt) cc_final: 0.8522 (ptp) REVERT: B 904 TYR cc_start: 0.7762 (m-10) cc_final: 0.7027 (m-10) REVERT: C 765 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7714 (mtp85) outliers start: 10 outliers final: 3 residues processed: 113 average time/residue: 0.7279 time to fit residues: 87.0081 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 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 = 0.3606 r_free = 0.3606 target = 0.144153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111655 restraints weight = 9612.678| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.76 r_work: 0.3056 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9744 Z= 0.180 Angle : 0.583 9.789 13371 Z= 0.298 Chirality : 0.042 0.127 1650 Planarity : 0.004 0.041 1698 Dihedral : 4.041 19.453 1893 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.95 % Allowed : 14.76 % Favored : 84.29 % 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: 1.49 (0.23), residues: 1248 helix: 2.55 (0.22), residues: 579 sheet: 0.73 (0.38), residues: 159 loop : -0.83 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1014 TYR 0.019 0.002 TYR C1067 PHE 0.014 0.002 PHE C 817 TRP 0.011 0.002 TRP B 886 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9696) covalent geometry : angle 0.56797 (13248) SS BOND : bond 0.00338 ( 21) SS BOND : angle 1.39502 ( 42) hydrogen bonds : bond 0.06013 ( 567) hydrogen bonds : angle 4.75631 ( 1647) link_BETA1-4 : bond 0.00485 ( 9) link_BETA1-4 : angle 1.16169 ( 27) link_NAG-ASN : bond 0.00236 ( 18) link_NAG-ASN : angle 1.72395 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.272 Fit side-chains REVERT: A 725 GLU cc_start: 0.8565 (tt0) cc_final: 0.8201 (tt0) REVERT: B 731 MET cc_start: 0.8908 (ptt) cc_final: 0.8469 (ptp) REVERT: B 904 TYR cc_start: 0.7824 (m-10) cc_final: 0.7108 (m-10) REVERT: C 765 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7775 (mtp85) REVERT: C 815 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7435 (mtp180) outliers start: 8 outliers final: 4 residues processed: 112 average time/residue: 0.5841 time to fit residues: 69.1874 Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 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 = 0.3642 r_free = 0.3642 target = 0.147026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115016 restraints weight = 9597.888| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.74 r_work: 0.3118 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9744 Z= 0.125 Angle : 0.518 9.191 13371 Z= 0.265 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.800 19.939 1893 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.43 % Allowed : 14.40 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.23), residues: 1248 helix: 2.63 (0.21), residues: 597 sheet: 1.52 (0.41), residues: 123 loop : -0.74 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.016 0.001 TYR C1067 PHE 0.013 0.001 PHE C 817 TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9696) covalent geometry : angle 0.50434 (13248) SS BOND : bond 0.00296 ( 21) SS BOND : angle 1.27354 ( 42) hydrogen bonds : bond 0.05150 ( 567) hydrogen bonds : angle 4.61142 ( 1647) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.06416 ( 27) link_NAG-ASN : bond 0.00247 ( 18) link_NAG-ASN : angle 1.51400 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.50 seconds wall clock time: 55 minutes 57.63 seconds (3357.63 seconds total)