Starting phenix.real_space_refine on Tue Feb 3 23:49:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6h_47565/02_2026/9e6h_47565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6h_47565/02_2026/9e6h_47565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6h_47565/02_2026/9e6h_47565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6h_47565/02_2026/9e6h_47565.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6h_47565/02_2026/9e6h_47565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6h_47565/02_2026/9e6h_47565.cif" } resolution = 2.84 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= -0.000 sd= 0.018 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 4 7.51 5 S 4 5.16 5 C 5122 2.51 5 N 1230 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8106 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1883 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1893 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 14, 'TRANS': 231} Chain: "C" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1883 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "D" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1883 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "E" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8106 At special positions: 0 Unit cell: (97.65, 84.63, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 Ca 4 19.99 S 4 16.00 O 1742 8.00 N 1230 7.00 C 5122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS C 272 " distance=2.11 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS D 272 " distance=1.95 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 E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 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 L 2 " - " BMA L 3 " NAG-ASN " NAG A 301 " - " ASN A 90 " " NAG A 302 " - " ASN A 220 " " NAG B 301 " - " ASN B 90 " " NAG B 302 " - " ASN B 220 " " NAG C 301 " - " ASN C 90 " " NAG C 302 " - " ASN C 220 " " NAG D 301 " - " ASN D 90 " " NAG D 302 " - " ASN D 220 " " NAG E 1 " - " ASN A 142 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN B 142 " " NAG H 1 " - " ASN B 208 " " NAG I 1 " - " ASN C 142 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 142 " " NAG L 1 " - " ASN D 208 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 210.1 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 4.5% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.685A pdb=" N ILE A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL A 254 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.685A pdb=" N ILE B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL B 254 " --> pdb=" O PRO B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.686A pdb=" N ILE C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL C 254 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.686A pdb=" N ILE D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL D 254 " --> pdb=" O PRO D 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 229 removed outlier: 4.509A pdb=" N GLY A 196 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 106 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 261 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 105 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL A 259 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS A 107 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS A 257 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS D 257 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 107 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL D 259 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL D 105 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 261 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL D 106 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY D 196 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL A 242 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL A 242 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 117 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 118 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 186 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 229 removed outlier: 4.509A pdb=" N GLY B 196 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 106 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 261 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 105 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL B 259 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS B 107 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS B 257 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS C 257 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS C 107 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL C 259 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 105 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 261 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 106 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY C 196 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL B 242 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL B 242 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 117 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 118 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 186 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB2, first strand: chain 'C' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL C 242 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL C 242 " --> pdb=" O TYR C 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 117 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 118 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 186 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL D 242 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL D 242 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 117 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 118 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 186 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 67 392 hydrogen bonds defined for protein. 1032 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: 1.19 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1310 1.31 - 1.43: 2330 1.43 - 1.56: 4662 1.56 - 1.68: 0 1.68 - 1.81: 4 Bond restraints: 8306 Sorted by residual: bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.490 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C7 NAG G 1 " pdb=" N2 NAG G 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C7 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C7 NAG K 1 " pdb=" N2 NAG K 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C7 NAG I 1 " pdb=" N2 NAG I 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 10933 2.27 - 4.54: 374 4.54 - 6.81: 70 6.81 - 9.08: 13 9.08 - 11.35: 4 Bond angle restraints: 11394 Sorted by residual: angle pdb=" C3 NAG E 2 " pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 107.29 118.64 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 107.29 118.63 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3 NAG I 2 " pdb=" C4 NAG I 2 " pdb=" O4 NAG I 2 " ideal model delta sigma weight residual 107.29 118.61 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C3 NAG G 2 " pdb=" C4 NAG G 2 " pdb=" O4 NAG G 2 " ideal model delta sigma weight residual 107.29 118.61 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C2 NAG J 1 " pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 110.06 117.81 -7.75 3.00e+00 1.11e-01 6.67e+00 ... (remaining 11389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.21: 5020 23.21 - 46.42: 212 46.42 - 69.63: 40 69.63 - 92.85: 60 92.85 - 116.06: 36 Dihedral angle restraints: 5368 sinusoidal: 2518 harmonic: 2850 Sorted by residual: dihedral pdb=" C2 MAN J 4 " pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " pdb=" C5 MAN J 4 " ideal model delta sinusoidal sigma weight residual -57.62 58.44 -116.06 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual -57.62 58.41 -116.03 1 3.00e+01 1.11e-03 1.53e+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 58.41 -116.03 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 989 0.043 - 0.086: 258 0.086 - 0.128: 127 0.128 - 0.171: 36 0.171 - 0.214: 16 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 208 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 208 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1423 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 217 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO D 218 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 218 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 218 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 217 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO C 218 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 217 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 218 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.021 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 144 2.65 - 3.21: 7488 3.21 - 3.77: 11924 3.77 - 4.34: 17372 4.34 - 4.90: 29334 Nonbonded interactions: 66262 Sorted by model distance: nonbonded pdb=" O3 NAG G 2 " pdb=" O5 BMA G 3 " model vdw 2.087 3.040 nonbonded pdb=" O3 NAG E 2 " pdb=" O5 BMA E 3 " model vdw 2.087 3.040 nonbonded pdb=" O3 NAG I 2 " pdb=" O5 BMA I 3 " model vdw 2.088 3.040 nonbonded pdb=" O3 NAG K 2 " pdb=" O5 BMA K 3 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU C 156 " pdb="MN MN C 304 " model vdw 2.142 2.320 ... (remaining 66257 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 'A' selection = (chain 'B' and (resid 30 through 273 or resid 301 through 304)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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: 0.770 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.014 0.144 8352 Z= 0.701 Angle : 0.989 15.853 11530 Z= 0.396 Chirality : 0.054 0.214 1426 Planarity : 0.005 0.038 1410 Dihedral : 19.317 116.057 3526 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 are not related in a simple way. whole: 0.47 (0.27), residues: 970 helix: -2.66 (0.57), residues: 24 sheet: 0.83 (0.25), residues: 464 loop : 0.04 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 65 TYR 0.005 0.001 TYR C 165 PHE 0.008 0.001 PHE C 102 TRP 0.011 0.001 TRP D 262 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.01399 ( 8306) covalent geometry : angle 0.92368 (11394) SS BOND : bond 0.08370 ( 2) SS BOND : angle 1.67655 ( 4) hydrogen bonds : bond 0.12265 ( 320) hydrogen bonds : angle 6.24159 ( 1032) link_ALPHA1-3 : bond 0.00315 ( 8) link_ALPHA1-3 : angle 0.88750 ( 24) link_ALPHA1-6 : bond 0.00504 ( 4) link_ALPHA1-6 : angle 1.04193 ( 12) link_BETA1-4 : bond 0.01519 ( 16) link_BETA1-4 : angle 5.31466 ( 48) link_NAG-ASN : bond 0.00181 ( 16) link_NAG-ASN : angle 1.81767 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 107 LYS cc_start: 0.8325 (tttp) cc_final: 0.8099 (tttm) REVERT: C 72 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8132 (mm-40) REVERT: C 107 LYS cc_start: 0.8499 (tttp) cc_final: 0.8257 (tttm) REVERT: D 48 LEU cc_start: 0.8854 (mt) cc_final: 0.8626 (mt) REVERT: D 89 ASP cc_start: 0.7689 (t0) cc_final: 0.7427 (t0) outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.5400 time to fit residues: 80.6737 Evaluate side-chains 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0470 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN B 128 GLN C 50 GLN D 62 GLN D 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.070236 restraints weight = 13658.374| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.75 r_work: 0.2777 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8352 Z= 0.173 Angle : 0.873 19.455 11530 Z= 0.365 Chirality : 0.053 0.306 1426 Planarity : 0.005 0.042 1410 Dihedral : 18.940 105.350 1920 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.95 % Allowed : 8.21 % Favored : 90.83 % 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 are not related in a simple way. whole: 0.59 (0.27), residues: 970 helix: -2.10 (0.64), residues: 24 sheet: 0.96 (0.25), residues: 464 loop : 0.04 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.012 0.001 TYR B 121 PHE 0.014 0.002 PHE A 98 TRP 0.013 0.001 TRP A 262 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8306) covalent geometry : angle 0.73630 (11394) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.19936 ( 4) hydrogen bonds : bond 0.03644 ( 320) hydrogen bonds : angle 4.98904 ( 1032) link_ALPHA1-3 : bond 0.00742 ( 8) link_ALPHA1-3 : angle 3.14071 ( 24) link_ALPHA1-6 : bond 0.01047 ( 4) link_ALPHA1-6 : angle 2.04268 ( 12) link_BETA1-4 : bond 0.02280 ( 16) link_BETA1-4 : angle 6.33868 ( 48) link_NAG-ASN : bond 0.00274 ( 16) link_NAG-ASN : angle 2.85731 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.290 Fit side-chains REVERT: A 147 ASP cc_start: 0.8002 (t0) cc_final: 0.7752 (t0) REVERT: A 189 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.8937 (tt0) REVERT: A 269 GLU cc_start: 0.7730 (pp20) cc_final: 0.7384 (pp20) REVERT: B 52 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 65 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7572 (ptm160) REVERT: B 72 GLN cc_start: 0.8122 (mm110) cc_final: 0.7174 (mm110) REVERT: B 107 LYS cc_start: 0.8356 (tttp) cc_final: 0.8154 (tttm) REVERT: B 147 ASP cc_start: 0.8148 (t0) cc_final: 0.7806 (t0) REVERT: B 269 GLU cc_start: 0.8038 (pm20) cc_final: 0.7823 (pm20) REVERT: C 52 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: C 65 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.7406 (ptm160) REVERT: C 67 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7875 (mp0) REVERT: C 72 GLN cc_start: 0.8628 (mm-40) cc_final: 0.7399 (mp10) REVERT: C 107 LYS cc_start: 0.8392 (tttp) cc_final: 0.8183 (tttm) REVERT: C 147 ASP cc_start: 0.8241 (t0) cc_final: 0.7940 (t0) REVERT: D 48 LEU cc_start: 0.9094 (mt) cc_final: 0.8892 (mt) REVERT: D 147 ASP cc_start: 0.8057 (t0) cc_final: 0.7786 (t0) REVERT: D 189 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.8833 (tt0) REVERT: D 269 GLU cc_start: 0.7749 (pp20) cc_final: 0.7458 (pp20) outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 0.5346 time to fit residues: 64.9153 Evaluate side-chains 104 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.062563 restraints weight = 13536.506| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.96 r_work: 0.2648 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8352 Z= 0.171 Angle : 0.819 18.245 11530 Z= 0.346 Chirality : 0.054 0.321 1426 Planarity : 0.004 0.044 1410 Dihedral : 17.379 106.176 1918 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.67 % Allowed : 8.93 % Favored : 89.40 % 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 are not related in a simple way. whole: 0.70 (0.28), residues: 970 helix: -1.74 (0.73), residues: 24 sheet: 0.98 (0.26), residues: 464 loop : 0.16 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 65 TYR 0.013 0.001 TYR B 121 PHE 0.015 0.002 PHE B 161 TRP 0.011 0.001 TRP D 262 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8306) covalent geometry : angle 0.69300 (11394) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.17420 ( 4) hydrogen bonds : bond 0.03682 ( 320) hydrogen bonds : angle 4.73943 ( 1032) link_ALPHA1-3 : bond 0.00895 ( 8) link_ALPHA1-3 : angle 2.72116 ( 24) link_ALPHA1-6 : bond 0.01532 ( 4) link_ALPHA1-6 : angle 1.48218 ( 12) link_BETA1-4 : bond 0.02354 ( 16) link_BETA1-4 : angle 6.03984 ( 48) link_NAG-ASN : bond 0.00248 ( 16) link_NAG-ASN : angle 2.55207 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.203 Fit side-chains REVERT: A 147 ASP cc_start: 0.8187 (t0) cc_final: 0.7923 (t0) REVERT: A 189 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.8966 (tt0) REVERT: A 269 GLU cc_start: 0.7770 (pp20) cc_final: 0.7371 (pp20) REVERT: B 65 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7866 (ttp-110) REVERT: B 67 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: B 72 GLN cc_start: 0.8539 (mm110) cc_final: 0.7525 (mm-40) REVERT: B 107 LYS cc_start: 0.8484 (tttp) cc_final: 0.8277 (tttm) REVERT: B 147 ASP cc_start: 0.8310 (t0) cc_final: 0.7867 (t0) REVERT: B 269 GLU cc_start: 0.8002 (pm20) cc_final: 0.7772 (pm20) REVERT: C 52 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8548 (pt0) REVERT: C 65 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.7989 (ptm160) REVERT: C 67 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8006 (mm-30) REVERT: C 72 GLN cc_start: 0.8793 (mm-40) cc_final: 0.7870 (mm-40) REVERT: C 147 ASP cc_start: 0.8347 (t0) cc_final: 0.7993 (t0) REVERT: D 147 ASP cc_start: 0.8238 (t0) cc_final: 0.7970 (t0) REVERT: D 189 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.8949 (tt0) REVERT: D 269 GLU cc_start: 0.7739 (pp20) cc_final: 0.7358 (pp20) outliers start: 14 outliers final: 4 residues processed: 113 average time/residue: 0.5516 time to fit residues: 65.5472 Evaluate side-chains 104 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 0.0040 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.066160 restraints weight = 14049.267| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.79 r_work: 0.2669 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8352 Z= 0.136 Angle : 0.817 18.344 11530 Z= 0.339 Chirality : 0.054 0.323 1426 Planarity : 0.004 0.043 1410 Dihedral : 16.165 106.072 1918 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.83 % Allowed : 10.71 % Favored : 88.45 % 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 are not related in a simple way. whole: 0.79 (0.28), residues: 970 helix: -1.67 (0.72), residues: 24 sheet: 1.03 (0.26), residues: 464 loop : 0.23 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.012 0.001 TYR C 121 PHE 0.015 0.001 PHE C 161 TRP 0.006 0.001 TRP D 262 HIS 0.001 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8306) covalent geometry : angle 0.68750 (11394) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.10804 ( 4) hydrogen bonds : bond 0.03190 ( 320) hydrogen bonds : angle 4.51361 ( 1032) link_ALPHA1-3 : bond 0.00884 ( 8) link_ALPHA1-3 : angle 2.82268 ( 24) link_ALPHA1-6 : bond 0.01542 ( 4) link_ALPHA1-6 : angle 1.66512 ( 12) link_BETA1-4 : bond 0.02435 ( 16) link_BETA1-4 : angle 6.02456 ( 48) link_NAG-ASN : bond 0.00150 ( 16) link_NAG-ASN : angle 2.67420 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.234 Fit side-chains REVERT: A 147 ASP cc_start: 0.8264 (t0) cc_final: 0.7944 (t0) REVERT: A 189 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.8873 (tt0) REVERT: A 269 GLU cc_start: 0.7767 (pp20) cc_final: 0.7411 (pp20) REVERT: B 65 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7756 (ptm160) REVERT: B 67 GLU cc_start: 0.7659 (mp0) cc_final: 0.6657 (mp0) REVERT: B 72 GLN cc_start: 0.8558 (mm110) cc_final: 0.7531 (mm-40) REVERT: B 147 ASP cc_start: 0.8291 (t0) cc_final: 0.7840 (t0) REVERT: B 156 GLU cc_start: 0.9065 (pt0) cc_final: 0.8862 (pt0) REVERT: B 269 GLU cc_start: 0.8017 (pm20) cc_final: 0.7813 (pm20) REVERT: C 52 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (pt0) REVERT: C 65 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.7920 (ptm160) REVERT: C 67 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7982 (mm-30) REVERT: C 72 GLN cc_start: 0.8810 (mm-40) cc_final: 0.7839 (mm-40) REVERT: C 147 ASP cc_start: 0.8367 (t0) cc_final: 0.7992 (t0) REVERT: D 147 ASP cc_start: 0.8323 (t0) cc_final: 0.8034 (t0) REVERT: D 189 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.8851 (tt0) REVERT: D 269 GLU cc_start: 0.7736 (pp20) cc_final: 0.7326 (pp20) outliers start: 7 outliers final: 3 residues processed: 104 average time/residue: 0.5993 time to fit residues: 65.4128 Evaluate side-chains 96 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN D 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.065408 restraints weight = 13838.218| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.75 r_work: 0.2656 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8352 Z= 0.142 Angle : 0.815 18.213 11530 Z= 0.338 Chirality : 0.054 0.322 1426 Planarity : 0.004 0.044 1410 Dihedral : 15.133 105.868 1918 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.95 % Allowed : 11.07 % Favored : 87.98 % 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 are not related in a simple way. whole: 0.87 (0.29), residues: 970 helix: -1.59 (0.77), residues: 24 sheet: 1.05 (0.26), residues: 464 loop : 0.33 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.013 0.001 TYR C 121 PHE 0.018 0.001 PHE B 161 TRP 0.006 0.001 TRP C 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8306) covalent geometry : angle 0.68753 (11394) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.13568 ( 4) hydrogen bonds : bond 0.03162 ( 320) hydrogen bonds : angle 4.39770 ( 1032) link_ALPHA1-3 : bond 0.00996 ( 8) link_ALPHA1-3 : angle 2.73552 ( 24) link_ALPHA1-6 : bond 0.01632 ( 4) link_ALPHA1-6 : angle 1.42933 ( 12) link_BETA1-4 : bond 0.02413 ( 16) link_BETA1-4 : angle 5.98831 ( 48) link_NAG-ASN : bond 0.00175 ( 16) link_NAG-ASN : angle 2.69603 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.176 Fit side-chains REVERT: A 147 ASP cc_start: 0.8339 (t0) cc_final: 0.8028 (t0) REVERT: A 269 GLU cc_start: 0.7776 (pp20) cc_final: 0.7389 (pp20) REVERT: B 65 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7814 (ttp-110) REVERT: B 67 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: B 72 GLN cc_start: 0.8623 (mm110) cc_final: 0.7418 (mm-40) REVERT: B 112 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: B 147 ASP cc_start: 0.8339 (t0) cc_final: 0.7917 (t0) REVERT: C 65 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.8265 (ttp-110) REVERT: C 72 GLN cc_start: 0.8816 (mm-40) cc_final: 0.7983 (mm-40) REVERT: C 112 ASP cc_start: 0.8949 (m-30) cc_final: 0.8602 (p0) REVERT: C 147 ASP cc_start: 0.8413 (t0) cc_final: 0.8019 (t0) REVERT: D 147 ASP cc_start: 0.8377 (t0) cc_final: 0.8049 (t0) REVERT: D 189 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.8853 (tt0) REVERT: D 269 GLU cc_start: 0.7767 (pp20) cc_final: 0.7338 (pp20) outliers start: 8 outliers final: 3 residues processed: 102 average time/residue: 0.6025 time to fit residues: 64.5310 Evaluate side-chains 105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.063878 restraints weight = 13826.398| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.69 r_work: 0.2625 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8352 Z= 0.165 Angle : 0.833 18.191 11530 Z= 0.348 Chirality : 0.054 0.326 1426 Planarity : 0.004 0.046 1410 Dihedral : 14.208 104.754 1918 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.71 % Allowed : 12.38 % Favored : 86.90 % 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 are not related in a simple way. whole: 0.88 (0.29), residues: 970 helix: -1.81 (0.73), residues: 24 sheet: 1.04 (0.26), residues: 464 loop : 0.36 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.016 0.001 TYR B 121 PHE 0.018 0.002 PHE C 161 TRP 0.007 0.001 TRP B 190 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8306) covalent geometry : angle 0.70782 (11394) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.17367 ( 4) hydrogen bonds : bond 0.03410 ( 320) hydrogen bonds : angle 4.45907 ( 1032) link_ALPHA1-3 : bond 0.00865 ( 8) link_ALPHA1-3 : angle 2.73330 ( 24) link_ALPHA1-6 : bond 0.01553 ( 4) link_ALPHA1-6 : angle 1.23477 ( 12) link_BETA1-4 : bond 0.02437 ( 16) link_BETA1-4 : angle 6.04553 ( 48) link_NAG-ASN : bond 0.00202 ( 16) link_NAG-ASN : angle 2.67753 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.263 Fit side-chains REVERT: A 147 ASP cc_start: 0.8398 (t0) cc_final: 0.8043 (t0) REVERT: A 269 GLU cc_start: 0.7776 (pp20) cc_final: 0.7372 (pp20) REVERT: B 65 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7990 (ttp-110) REVERT: B 67 GLU cc_start: 0.7706 (mp0) cc_final: 0.6605 (mp0) REVERT: B 72 GLN cc_start: 0.8639 (mm110) cc_final: 0.7473 (mm-40) REVERT: C 65 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.7960 (ttp-110) REVERT: C 67 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7741 (mp0) REVERT: C 74 TYR cc_start: 0.9169 (m-80) cc_final: 0.8967 (m-80) REVERT: C 112 ASP cc_start: 0.8967 (m-30) cc_final: 0.8595 (p0) REVERT: C 147 ASP cc_start: 0.8420 (t0) cc_final: 0.8130 (t0) REVERT: D 147 ASP cc_start: 0.8397 (t0) cc_final: 0.8058 (t0) REVERT: D 269 GLU cc_start: 0.7784 (pp20) cc_final: 0.7338 (pp20) outliers start: 6 outliers final: 5 residues processed: 105 average time/residue: 0.6267 time to fit residues: 68.9936 Evaluate side-chains 107 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.061164 restraints weight = 13901.098| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.70 r_work: 0.2549 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8352 Z= 0.196 Angle : 0.849 18.308 11530 Z= 0.359 Chirality : 0.054 0.331 1426 Planarity : 0.004 0.045 1410 Dihedral : 13.256 104.115 1918 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.07 % Allowed : 12.26 % Favored : 86.67 % 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 are not related in a simple way. whole: 0.88 (0.29), residues: 970 helix: -2.04 (0.71), residues: 24 sheet: 0.87 (0.26), residues: 458 loop : 0.60 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.019 0.001 TYR C 121 PHE 0.018 0.002 PHE B 161 TRP 0.009 0.001 TRP C 190 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8306) covalent geometry : angle 0.72503 (11394) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.23569 ( 4) hydrogen bonds : bond 0.03682 ( 320) hydrogen bonds : angle 4.59871 ( 1032) link_ALPHA1-3 : bond 0.00826 ( 8) link_ALPHA1-3 : angle 2.70503 ( 24) link_ALPHA1-6 : bond 0.01517 ( 4) link_ALPHA1-6 : angle 0.96531 ( 12) link_BETA1-4 : bond 0.02480 ( 16) link_BETA1-4 : angle 6.13295 ( 48) link_NAG-ASN : bond 0.00229 ( 16) link_NAG-ASN : angle 2.65094 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8428 (t0) cc_final: 0.8055 (t0) REVERT: A 269 GLU cc_start: 0.7775 (pp20) cc_final: 0.7324 (pp20) REVERT: B 52 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8724 (mt-10) REVERT: C 112 ASP cc_start: 0.8997 (m-30) cc_final: 0.8621 (p0) REVERT: D 147 ASP cc_start: 0.8472 (t0) cc_final: 0.8116 (t0) REVERT: D 269 GLU cc_start: 0.7820 (pp20) cc_final: 0.7293 (pp20) outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 0.6497 time to fit residues: 70.7866 Evaluate side-chains 100 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.063219 restraints weight = 13651.686| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.70 r_work: 0.2608 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8352 Z= 0.147 Angle : 0.831 18.197 11530 Z= 0.352 Chirality : 0.053 0.329 1426 Planarity : 0.004 0.045 1410 Dihedral : 12.846 104.772 1918 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.71 % Allowed : 12.98 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.29), residues: 970 helix: -1.90 (0.75), residues: 24 sheet: 0.86 (0.26), residues: 458 loop : 0.59 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 65 TYR 0.016 0.001 TYR B 121 PHE 0.017 0.001 PHE B 161 TRP 0.006 0.001 TRP D 190 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8306) covalent geometry : angle 0.70568 (11394) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.12786 ( 4) hydrogen bonds : bond 0.03300 ( 320) hydrogen bonds : angle 4.41787 ( 1032) link_ALPHA1-3 : bond 0.00839 ( 8) link_ALPHA1-3 : angle 2.54700 ( 24) link_ALPHA1-6 : bond 0.01474 ( 4) link_ALPHA1-6 : angle 0.94006 ( 12) link_BETA1-4 : bond 0.02428 ( 16) link_BETA1-4 : angle 6.07304 ( 48) link_NAG-ASN : bond 0.00139 ( 16) link_NAG-ASN : angle 2.68189 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.293 Fit side-chains REVERT: A 65 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.8636 (ttp-110) REVERT: A 147 ASP cc_start: 0.8400 (t0) cc_final: 0.8023 (t0) REVERT: A 269 GLU cc_start: 0.7726 (pp20) cc_final: 0.7263 (pp20) REVERT: B 52 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 65 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8077 (ttp-110) REVERT: B 67 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7611 (mp0) REVERT: C 67 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7694 (mp0) REVERT: C 112 ASP cc_start: 0.8995 (m-30) cc_final: 0.8617 (p0) REVERT: D 147 ASP cc_start: 0.8446 (t0) cc_final: 0.8088 (t0) REVERT: D 269 GLU cc_start: 0.7749 (pp20) cc_final: 0.7234 (pp20) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.6562 time to fit residues: 68.7873 Evaluate side-chains 100 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0570 chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.063759 restraints weight = 13910.960| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.77 r_work: 0.2598 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8352 Z= 0.140 Angle : 0.811 18.195 11530 Z= 0.342 Chirality : 0.052 0.328 1426 Planarity : 0.004 0.045 1410 Dihedral : 12.200 103.466 1918 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.71 % Allowed : 13.10 % Favored : 86.19 % 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 are not related in a simple way. whole: 0.86 (0.29), residues: 970 helix: -1.85 (0.78), residues: 24 sheet: 0.85 (0.26), residues: 458 loop : 0.57 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 65 TYR 0.018 0.001 TYR B 121 PHE 0.017 0.001 PHE B 161 TRP 0.005 0.001 TRP C 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8306) covalent geometry : angle 0.68335 (11394) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.10998 ( 4) hydrogen bonds : bond 0.03086 ( 320) hydrogen bonds : angle 4.31354 ( 1032) link_ALPHA1-3 : bond 0.00865 ( 8) link_ALPHA1-3 : angle 2.31975 ( 24) link_ALPHA1-6 : bond 0.01404 ( 4) link_ALPHA1-6 : angle 1.33750 ( 12) link_BETA1-4 : bond 0.02462 ( 16) link_BETA1-4 : angle 6.03378 ( 48) link_NAG-ASN : bond 0.00134 ( 16) link_NAG-ASN : angle 2.72185 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.294 Fit side-chains REVERT: A 147 ASP cc_start: 0.8403 (t0) cc_final: 0.8032 (t0) REVERT: A 269 GLU cc_start: 0.7771 (pp20) cc_final: 0.7300 (pp20) REVERT: B 52 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8504 (mt-10) REVERT: B 65 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8234 (ttp-110) REVERT: C 65 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.7939 (ttp-110) REVERT: C 67 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7659 (mp0) REVERT: C 112 ASP cc_start: 0.8966 (m-30) cc_final: 0.8590 (p0) REVERT: D 147 ASP cc_start: 0.8443 (t0) cc_final: 0.8085 (t0) REVERT: D 269 GLU cc_start: 0.7802 (pp20) cc_final: 0.7283 (pp20) outliers start: 6 outliers final: 4 residues processed: 103 average time/residue: 0.6597 time to fit residues: 71.1655 Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.061673 restraints weight = 13853.025| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.75 r_work: 0.2561 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8352 Z= 0.181 Angle : 0.836 18.224 11530 Z= 0.356 Chirality : 0.052 0.332 1426 Planarity : 0.004 0.046 1410 Dihedral : 11.421 99.294 1918 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.36 % Allowed : 13.45 % Favored : 86.19 % 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 are not related in a simple way. whole: 0.80 (0.29), residues: 970 helix: -1.94 (0.77), residues: 24 sheet: 0.79 (0.26), residues: 458 loop : 0.55 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 65 TYR 0.024 0.001 TYR C 121 PHE 0.017 0.002 PHE B 161 TRP 0.008 0.001 TRP B 190 HIS 0.002 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8306) covalent geometry : angle 0.70945 (11394) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.23697 ( 4) hydrogen bonds : bond 0.03528 ( 320) hydrogen bonds : angle 4.46164 ( 1032) link_ALPHA1-3 : bond 0.00804 ( 8) link_ALPHA1-3 : angle 2.42091 ( 24) link_ALPHA1-6 : bond 0.01184 ( 4) link_ALPHA1-6 : angle 1.98550 ( 12) link_BETA1-4 : bond 0.02444 ( 16) link_BETA1-4 : angle 6.08814 ( 48) link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 2.69739 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.293 Fit side-chains REVERT: A 269 GLU cc_start: 0.7787 (pp20) cc_final: 0.7307 (pp20) REVERT: B 65 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8404 (ttp-110) REVERT: C 65 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8378 (ttp-110) REVERT: C 112 ASP cc_start: 0.8979 (m-30) cc_final: 0.8599 (p0) REVERT: C 147 ASP cc_start: 0.8512 (t0) cc_final: 0.8148 (t0) REVERT: D 147 ASP cc_start: 0.8454 (t0) cc_final: 0.8062 (t0) REVERT: D 269 GLU cc_start: 0.7834 (pp20) cc_final: 0.7303 (pp20) outliers start: 3 outliers final: 3 residues processed: 97 average time/residue: 0.6714 time to fit residues: 68.1554 Evaluate side-chains 97 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.061301 restraints weight = 13782.632| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.72 r_work: 0.2564 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8352 Z= 0.186 Angle : 0.840 18.184 11530 Z= 0.358 Chirality : 0.052 0.333 1426 Planarity : 0.004 0.045 1410 Dihedral : 10.936 96.430 1918 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.36 % Allowed : 13.69 % Favored : 85.95 % 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 are not related in a simple way. whole: 0.76 (0.29), residues: 970 helix: -2.03 (0.75), residues: 24 sheet: 0.78 (0.26), residues: 458 loop : 0.51 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 65 TYR 0.023 0.001 TYR C 121 PHE 0.017 0.002 PHE B 161 TRP 0.009 0.001 TRP B 190 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8306) covalent geometry : angle 0.71390 (11394) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.22327 ( 4) hydrogen bonds : bond 0.03585 ( 320) hydrogen bonds : angle 4.50588 ( 1032) link_ALPHA1-3 : bond 0.00790 ( 8) link_ALPHA1-3 : angle 2.42098 ( 24) link_ALPHA1-6 : bond 0.01045 ( 4) link_ALPHA1-6 : angle 2.31493 ( 12) link_BETA1-4 : bond 0.02423 ( 16) link_BETA1-4 : angle 6.08915 ( 48) link_NAG-ASN : bond 0.00184 ( 16) link_NAG-ASN : angle 2.65486 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.60 seconds wall clock time: 37 minutes 58.11 seconds (2278.11 seconds total)