Starting phenix.real_space_refine on Thu Jul 2 08:56:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6h_47565/07_2026/9e6h_47565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6h_47565/07_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_47565/07_2026/9e6h_47565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6h_47565/07_2026/9e6h_47565.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6h_47565/07_2026/9e6h_47565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6h_47565/07_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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 28 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 28 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 28 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.22, per 1000 atoms: 0.27 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: 0.96 Conformation dependent library (CDL) restraints added in 491.6 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: 0.31 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: 1.56 Time building geometry restraints manager: 1.20 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 3.060 ... (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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.210 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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/Z covalent geometry : bond 0.01399 / 0.70 ( 8306) covalent geometry : angle 0.92368 / 0.38 (11394) SS BOND : bond 0.08370 / 4.20 ( 2) SS BOND : angle 1.67655 / 0.73 ( 4) hydrogen bonds : bond 0.12265 / 8.27 ( 320) hydrogen bonds : angle 6.24159 / 4.31 ( 1032) link_ALPHA1-3 : bond 0.00315 / 0.20 ( 8) link_ALPHA1-3 : angle 0.88750 / 0.60 ( 24) link_ALPHA1-6 : bond 0.00504 / 0.25 ( 4) link_ALPHA1-6 : angle 1.04193 / 0.63 ( 12) link_BETA1-4 : bond 0.01519 / 0.93 ( 16) link_BETA1-4 : angle 5.31466 / 3.05 ( 48) link_NAG-ASN : bond 0.00181 / 0.13 ( 16) link_NAG-ASN : angle 1.81767 / 1.07 ( 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 : 0.267 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: 0.6481 time to fit residues: 96.5466 Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3577 r_free = 0.3577 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072585 restraints weight = 13486.979| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.88 r_work: 0.2818 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8352 Z= 0.158 Angle : 0.856 19.437 11530 Z= 0.357 Chirality : 0.053 0.273 1426 Planarity : 0.005 0.041 1410 Dihedral : 18.845 105.066 1920 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.07 % Allowed : 8.21 % Favored : 90.71 % 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 are not related in a simple way. whole: 0.60 (0.27), residues: 970 helix: -2.45 (0.54), residues: 24 sheet: 0.97 (0.25), residues: 464 loop : 0.06 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.012 0.001 TYR B 165 PHE 0.014 0.001 PHE A 98 TRP 0.011 0.001 TRP A 262 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 8306) covalent geometry : angle 0.71722 / 0.32 (11394) SS BOND : bond 0.00396 / 0.20 ( 2) SS BOND : angle 0.18057 / 0.10 ( 4) hydrogen bonds : bond 0.03488 / 2.37 ( 320) hydrogen bonds : angle 4.94130 / 3.45 ( 1032) link_ALPHA1-3 : bond 0.00887 / 0.53 ( 8) link_ALPHA1-3 : angle 3.01633 / 2.01 ( 24) link_ALPHA1-6 : bond 0.01325 / 0.67 ( 4) link_ALPHA1-6 : angle 1.99048 / 1.38 ( 12) link_BETA1-4 : bond 0.02179 / 1.32 ( 16) link_BETA1-4 : angle 6.34141 / 3.61 ( 48) link_NAG-ASN : bond 0.00094 / 0.06 ( 16) link_NAG-ASN : angle 2.88131 / 1.82 ( 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 120 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.205 Fit side-chains REVERT: A 147 ASP cc_start: 0.8008 (t0) cc_final: 0.7796 (t0) REVERT: A 189 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.8893 (tt0) REVERT: A 269 GLU cc_start: 0.7796 (pp20) cc_final: 0.7574 (pp20) REVERT: B 52 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: B 65 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7754 (ptm160) REVERT: B 72 GLN cc_start: 0.8123 (mm110) cc_final: 0.7491 (mm110) REVERT: B 107 LYS cc_start: 0.8417 (tttp) cc_final: 0.8211 (tttm) REVERT: B 147 ASP cc_start: 0.8101 (t0) cc_final: 0.7733 (t0) REVERT: B 269 GLU cc_start: 0.8117 (pm20) cc_final: 0.7904 (pm20) REVERT: C 52 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: C 65 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.7649 (ptm160) REVERT: C 72 GLN cc_start: 0.8653 (mm-40) cc_final: 0.7748 (mm-40) REVERT: C 107 LYS cc_start: 0.8476 (tttp) cc_final: 0.8263 (tttm) REVERT: C 147 ASP cc_start: 0.8223 (t0) cc_final: 0.7935 (t0) REVERT: D 147 ASP cc_start: 0.8096 (t0) cc_final: 0.7831 (t0) REVERT: D 189 GLN cc_start: 0.9432 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: D 269 GLU cc_start: 0.7800 (pp20) cc_final: 0.7513 (pp20) outliers start: 9 outliers final: 4 residues processed: 117 average time/residue: 0.5353 time to fit residues: 66.1322 Evaluate side-chains 109 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 52 GLU 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: 0.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN C 50 GLN D 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.068298 restraints weight = 13700.021| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.71 r_work: 0.2715 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2145 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= 0.157 Angle : 0.810 18.221 11530 Z= 0.340 Chirality : 0.054 0.316 1426 Planarity : 0.004 0.045 1410 Dihedral : 17.252 106.360 1918 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.55 % Allowed : 9.64 % Favored : 88.81 % 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: -2.27 (0.71), residues: 24 sheet: 1.00 (0.26), residues: 464 loop : 0.17 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 65 TYR 0.013 0.001 TYR B 121 PHE 0.015 0.001 PHE C 161 TRP 0.012 0.001 TRP D 262 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8306) covalent geometry : angle 0.68379 / 0.31 (11394) SS BOND : bond 0.00055 / 0.03 ( 2) SS BOND : angle 0.16874 / 0.10 ( 4) hydrogen bonds : bond 0.03475 / 2.36 ( 320) hydrogen bonds : angle 4.63465 / 3.22 ( 1032) link_ALPHA1-3 : bond 0.00901 / 0.52 ( 8) link_ALPHA1-3 : angle 2.60565 / 1.75 ( 24) link_ALPHA1-6 : bond 0.01508 / 0.76 ( 4) link_ALPHA1-6 : angle 1.45302 / 0.99 ( 12) link_BETA1-4 : bond 0.02372 / 1.46 ( 16) link_BETA1-4 : angle 6.02236 / 3.42 ( 48) link_NAG-ASN : bond 0.00203 / 0.13 ( 16) link_NAG-ASN : angle 2.56728 / 1.67 ( 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: 13 poor density : 107 time to evaluate : 0.286 Fit side-chains REVERT: A 147 ASP cc_start: 0.8112 (t0) cc_final: 0.7826 (t0) REVERT: A 189 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8860 (tt0) REVERT: A 269 GLU cc_start: 0.7757 (pp20) cc_final: 0.7444 (pp20) REVERT: B 52 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8463 (pt0) REVERT: B 65 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7386 (ptm160) REVERT: B 67 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7545 (mp0) REVERT: B 72 GLN cc_start: 0.8498 (mm110) cc_final: 0.7015 (mm110) REVERT: B 107 LYS cc_start: 0.8445 (tttp) cc_final: 0.8237 (tttm) REVERT: B 134 VAL cc_start: 0.9045 (p) cc_final: 0.8810 (t) REVERT: B 147 ASP cc_start: 0.8260 (t0) cc_final: 0.7825 (t0) REVERT: C 52 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: C 65 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7440 (ptm160) REVERT: C 67 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7477 (mp0) REVERT: C 72 GLN cc_start: 0.8753 (mm-40) cc_final: 0.7283 (mm-40) REVERT: C 112 ASP cc_start: 0.8955 (m-30) cc_final: 0.8578 (p0) REVERT: C 147 ASP cc_start: 0.8316 (t0) cc_final: 0.7975 (t0) REVERT: D 147 ASP cc_start: 0.8206 (t0) cc_final: 0.7920 (t0) REVERT: D 189 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.8844 (tt0) REVERT: D 253 GLU cc_start: 0.8883 (pt0) cc_final: 0.8605 (pt0) REVERT: D 269 GLU cc_start: 0.7764 (pp20) cc_final: 0.7399 (pp20) outliers start: 13 outliers final: 4 residues processed: 114 average time/residue: 0.5961 time to fit residues: 71.3371 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 52 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: 6.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN B 128 GLN C 50 GLN D 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.065805 restraints weight = 13993.819| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.74 r_work: 0.2661 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8352 Z= 0.161 Angle : 0.835 18.237 11530 Z= 0.350 Chirality : 0.055 0.329 1426 Planarity : 0.004 0.045 1410 Dihedral : 15.542 105.044 1918 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.19 % Allowed : 10.71 % 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 are not related in a simple way. whole: 0.80 (0.28), residues: 970 helix: -2.05 (0.84), residues: 24 sheet: 1.05 (0.26), residues: 464 loop : 0.25 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.015 0.001 TYR C 121 PHE 0.017 0.002 PHE C 161 TRP 0.009 0.001 TRP D 262 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8306) covalent geometry : angle 0.70925 / 0.32 (11394) SS BOND : bond 0.00040 / 0.02 ( 2) SS BOND : angle 0.19323 / 0.09 ( 4) hydrogen bonds : bond 0.03433 / 2.33 ( 320) hydrogen bonds : angle 4.53732 / 3.17 ( 1032) link_ALPHA1-3 : bond 0.00869 / 0.50 ( 8) link_ALPHA1-3 : angle 2.91484 / 1.96 ( 24) link_ALPHA1-6 : bond 0.01553 / 0.78 ( 4) link_ALPHA1-6 : angle 1.67992 / 1.14 ( 12) link_BETA1-4 : bond 0.02409 / 1.48 ( 16) link_BETA1-4 : angle 6.00393 / 3.40 ( 48) link_NAG-ASN : bond 0.00189 / 0.12 ( 16) link_NAG-ASN : angle 2.65835 / 1.73 ( 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 114 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.263 Fit side-chains REVERT: A 147 ASP cc_start: 0.8299 (t0) cc_final: 0.7990 (t0) REVERT: A 189 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.8880 (tt0) REVERT: A 269 GLU cc_start: 0.7748 (pp20) cc_final: 0.7378 (pp20) REVERT: B 52 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8552 (pt0) REVERT: B 65 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.8118 (ttp-110) REVERT: B 67 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7958 (mm-30) REVERT: B 72 GLN cc_start: 0.8547 (mm110) cc_final: 0.7844 (mm110) REVERT: B 156 GLU cc_start: 0.8528 (pt0) cc_final: 0.8254 (pt0) REVERT: C 65 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.7881 (ttp-110) REVERT: C 67 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7850 (mp0) REVERT: C 72 GLN cc_start: 0.8775 (mm-40) cc_final: 0.7881 (mm-40) REVERT: D 147 ASP cc_start: 0.8342 (t0) cc_final: 0.8012 (t0) REVERT: D 189 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: D 269 GLU cc_start: 0.7764 (pp20) cc_final: 0.7352 (pp20) outliers start: 10 outliers final: 4 residues processed: 109 average time/residue: 0.6348 time to fit residues: 72.6429 Evaluate side-chains 106 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 263 SER 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: 3.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 171 ASN A 221 GLN B 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.092661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.059085 restraints weight = 13775.652| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.85 r_work: 0.2668 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8352 Z= 0.224 Angle : 0.860 18.126 11530 Z= 0.367 Chirality : 0.055 0.325 1426 Planarity : 0.004 0.046 1410 Dihedral : 14.765 104.941 1918 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.95 % Allowed : 11.67 % Favored : 87.38 % 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: 0.81 (0.29), residues: 970 helix: -2.21 (0.86), residues: 24 sheet: 0.96 (0.26), residues: 470 loop : 0.37 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 65 TYR 0.016 0.001 TYR B 121 PHE 0.016 0.002 PHE B 161 TRP 0.010 0.001 TRP B 190 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 ( 8306) covalent geometry : angle 0.73911 / 0.34 (11394) SS BOND : bond 0.00138 / 0.07 ( 2) SS BOND : angle 0.26185 / 0.12 ( 4) hydrogen bonds : bond 0.03917 / 2.67 ( 320) hydrogen bonds : angle 4.69508 / 3.29 ( 1032) link_ALPHA1-3 : bond 0.00875 / 0.50 ( 8) link_ALPHA1-3 : angle 2.70805 / 1.86 ( 24) link_ALPHA1-6 : bond 0.01474 / 0.74 ( 4) link_ALPHA1-6 : angle 1.29667 / 0.92 ( 12) link_BETA1-4 : bond 0.02421 / 1.48 ( 16) link_BETA1-4 : angle 6.09965 / 3.45 ( 48) link_NAG-ASN : bond 0.00318 / 0.21 ( 16) link_NAG-ASN : angle 2.61569 / 1.71 ( 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 107 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.325 Fit side-chains REVERT: A 147 ASP cc_start: 0.8445 (t0) cc_final: 0.8130 (t0) REVERT: A 269 GLU cc_start: 0.7851 (pp20) cc_final: 0.7459 (pp20) REVERT: B 52 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8710 (pt0) REVERT: B 65 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8159 (ttp-110) REVERT: B 121 TYR cc_start: 0.9323 (p90) cc_final: 0.9085 (p90) REVERT: C 65 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8101 (ttp-110) REVERT: C 67 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8141 (mm-30) REVERT: C 112 ASP cc_start: 0.9011 (m-30) cc_final: 0.8658 (p0) REVERT: D 147 ASP cc_start: 0.8472 (t0) cc_final: 0.8147 (t0) REVERT: D 269 GLU cc_start: 0.7882 (pp20) cc_final: 0.7437 (pp20) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.6658 time to fit residues: 72.6123 Evaluate side-chains 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.063129 restraints weight = 13683.040| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.71 r_work: 0.2611 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3187 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= 0.156 Angle : 0.838 18.198 11530 Z= 0.351 Chirality : 0.054 0.328 1426 Planarity : 0.004 0.046 1410 Dihedral : 14.163 105.372 1918 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.83 % Allowed : 12.62 % Favored : 86.55 % 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 (0.29), residues: 970 helix: -2.28 (0.85), residues: 24 sheet: 0.86 (0.26), residues: 453 loop : 0.48 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 65 TYR 0.008 0.001 TYR A 165 PHE 0.016 0.002 PHE B 161 TRP 0.007 0.001 TRP C 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8306) covalent geometry : angle 0.71169 / 0.32 (11394) SS BOND : bond 0.00084 / 0.04 ( 2) SS BOND : angle 0.13672 / 0.06 ( 4) hydrogen bonds : bond 0.03457 / 2.34 ( 320) hydrogen bonds : angle 4.52030 / 3.14 ( 1032) link_ALPHA1-3 : bond 0.00871 / 0.50 ( 8) link_ALPHA1-3 : angle 2.77946 / 1.90 ( 24) link_ALPHA1-6 : bond 0.01534 / 0.77 ( 4) link_ALPHA1-6 : angle 1.24895 / 0.89 ( 12) link_BETA1-4 : bond 0.02441 / 1.50 ( 16) link_BETA1-4 : angle 6.08203 / 3.43 ( 48) link_NAG-ASN : bond 0.00180 / 0.12 ( 16) link_NAG-ASN : angle 2.67790 / 1.74 ( 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 105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.248 Fit side-chains REVERT: A 116 ASP cc_start: 0.7385 (m-30) cc_final: 0.7161 (m-30) REVERT: A 147 ASP cc_start: 0.8415 (t0) cc_final: 0.8085 (t0) REVERT: A 269 GLU cc_start: 0.7754 (pp20) cc_final: 0.7336 (pp20) REVERT: B 52 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8631 (pt0) REVERT: C 65 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8077 (ttp-110) REVERT: C 67 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8006 (mp0) REVERT: C 112 ASP cc_start: 0.9000 (m-30) cc_final: 0.8614 (p0) REVERT: D 116 ASP cc_start: 0.7420 (m-30) cc_final: 0.7162 (m-30) REVERT: D 147 ASP cc_start: 0.8443 (t0) cc_final: 0.8105 (t0) REVERT: D 269 GLU cc_start: 0.7792 (pp20) cc_final: 0.7318 (pp20) outliers start: 7 outliers final: 4 residues processed: 102 average time/residue: 0.6528 time to fit residues: 69.8272 Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER 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: 2.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 9 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.062925 restraints weight = 13747.162| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.69 r_work: 0.2610 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3311 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 : 0.840 18.167 11530 Z= 0.353 Chirality : 0.054 0.328 1426 Planarity : 0.004 0.046 1410 Dihedral : 13.440 105.314 1918 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.07 % Allowed : 12.74 % 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: 0.82 (0.29), residues: 970 helix: -2.43 (0.80), residues: 24 sheet: 0.86 (0.26), residues: 453 loop : 0.53 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 65 TYR 0.011 0.001 TYR B 121 PHE 0.018 0.002 PHE B 161 TRP 0.007 0.001 TRP B 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8306) covalent geometry : angle 0.71515 / 0.32 (11394) SS BOND : bond 0.00107 / 0.05 ( 2) SS BOND : angle 0.17273 / 0.08 ( 4) hydrogen bonds : bond 0.03421 / 2.32 ( 320) hydrogen bonds : angle 4.47562 / 3.12 ( 1032) link_ALPHA1-3 : bond 0.00843 / 0.49 ( 8) link_ALPHA1-3 : angle 2.66778 / 1.84 ( 24) link_ALPHA1-6 : bond 0.01526 / 0.77 ( 4) link_ALPHA1-6 : angle 1.01336 / 0.75 ( 12) link_BETA1-4 : bond 0.02418 / 1.49 ( 16) link_BETA1-4 : angle 6.09760 / 3.44 ( 48) link_NAG-ASN : bond 0.00188 / 0.12 ( 16) link_NAG-ASN : angle 2.69035 / 1.75 ( 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 104 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.280 Fit side-chains REVERT: A 147 ASP cc_start: 0.8431 (t0) cc_final: 0.8054 (t0) REVERT: A 269 GLU cc_start: 0.7780 (pp20) cc_final: 0.7317 (pp20) REVERT: B 65 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8241 (ttp-110) REVERT: B 67 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7737 (mp0) REVERT: C 67 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8189 (mm-30) REVERT: D 147 ASP cc_start: 0.8465 (t0) cc_final: 0.8101 (t0) REVERT: D 269 GLU cc_start: 0.7793 (pp20) cc_final: 0.7269 (pp20) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.6370 time to fit residues: 68.0307 Evaluate side-chains 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.062901 restraints weight = 13539.125| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.67 r_work: 0.2574 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3405 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= 0.166 Angle : 0.837 18.226 11530 Z= 0.352 Chirality : 0.053 0.330 1426 Planarity : 0.004 0.045 1410 Dihedral : 12.970 104.798 1918 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.71 % Allowed : 12.50 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.29), residues: 970 helix: -2.44 (0.81), residues: 24 sheet: 0.83 (0.26), residues: 453 loop : 0.52 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 65 TYR 0.009 0.001 TYR B 74 PHE 0.016 0.002 PHE B 161 TRP 0.008 0.001 TRP C 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 8306) covalent geometry : angle 0.71152 / 0.32 (11394) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 0.16976 / 0.08 ( 4) hydrogen bonds : bond 0.03415 / 2.31 ( 320) hydrogen bonds : angle 4.46897 / 3.11 ( 1032) link_ALPHA1-3 : bond 0.00817 / 0.47 ( 8) link_ALPHA1-3 : angle 2.60437 / 1.81 ( 24) link_ALPHA1-6 : bond 0.01486 / 0.74 ( 4) link_ALPHA1-6 : angle 0.91712 / 0.67 ( 12) link_BETA1-4 : bond 0.02443 / 1.50 ( 16) link_BETA1-4 : angle 6.10383 / 3.45 ( 48) link_NAG-ASN : bond 0.00178 / 0.11 ( 16) link_NAG-ASN : angle 2.68831 / 1.75 ( 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 103 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.212 Fit side-chains REVERT: A 147 ASP cc_start: 0.8436 (t0) cc_final: 0.8055 (t0) REVERT: A 269 GLU cc_start: 0.7752 (pp20) cc_final: 0.7265 (pp20) REVERT: B 65 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8405 (ttp-110) REVERT: B 67 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8093 (mm-30) REVERT: C 65 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8127 (ttp-110) REVERT: C 67 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8026 (mp0) REVERT: C 112 ASP cc_start: 0.9023 (m-30) cc_final: 0.8662 (p0) REVERT: C 189 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: D 147 ASP cc_start: 0.8461 (t0) cc_final: 0.8086 (t0) REVERT: D 269 GLU cc_start: 0.7787 (pp20) cc_final: 0.7260 (pp20) outliers start: 6 outliers final: 6 residues processed: 101 average time/residue: 0.6313 time to fit residues: 66.7327 Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 70 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 0.2826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.064729 restraints weight = 13495.048| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.71 r_work: 0.2632 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3442 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= 0.134 Angle : 0.816 18.202 11530 Z= 0.343 Chirality : 0.052 0.326 1426 Planarity : 0.004 0.045 1410 Dihedral : 12.611 104.666 1918 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.48 % Allowed : 13.10 % Favored : 86.43 % 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: 0.74 (0.29), residues: 970 helix: -2.47 (0.78), residues: 24 sheet: 0.84 (0.26), residues: 452 loop : 0.45 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 65 TYR 0.011 0.001 TYR D 250 PHE 0.019 0.001 PHE B 161 TRP 0.005 0.001 TRP B 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8306) covalent geometry : angle 0.68961 / 0.31 (11394) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 0.06725 / 0.03 ( 4) hydrogen bonds : bond 0.03048 / 2.06 ( 320) hydrogen bonds : angle 4.33162 / 3.00 ( 1032) link_ALPHA1-3 : bond 0.00856 / 0.50 ( 8) link_ALPHA1-3 : angle 2.41359 / 1.68 ( 24) link_ALPHA1-6 : bond 0.01476 / 0.74 ( 4) link_ALPHA1-6 : angle 1.01727 / 0.66 ( 12) link_BETA1-4 : bond 0.02462 / 1.51 ( 16) link_BETA1-4 : angle 6.05131 / 3.42 ( 48) link_NAG-ASN : bond 0.00130 / 0.08 ( 16) link_NAG-ASN : angle 2.72885 / 1.77 ( 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 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.274 Fit side-chains REVERT: A 65 ARG cc_start: 0.8629 (ptm-80) cc_final: 0.8416 (ptm-80) REVERT: A 147 ASP cc_start: 0.8375 (t0) cc_final: 0.7989 (t0) REVERT: A 269 GLU cc_start: 0.7729 (pp20) cc_final: 0.7245 (pp20) REVERT: B 65 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8412 (ttp-110) REVERT: B 67 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8089 (mm-30) REVERT: B 156 GLU cc_start: 0.8455 (pt0) cc_final: 0.7969 (pt0) REVERT: C 65 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: C 67 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 112 ASP cc_start: 0.8984 (m-30) cc_final: 0.8618 (p0) REVERT: D 147 ASP cc_start: 0.8416 (t0) cc_final: 0.8043 (t0) REVERT: D 269 GLU cc_start: 0.7782 (pp20) cc_final: 0.7249 (pp20) outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.6526 time to fit residues: 67.8130 Evaluate side-chains 96 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.0970 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.062168 restraints weight = 13696.351| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.69 r_work: 0.2543 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8352 Z= 0.177 Angle : 0.831 18.173 11530 Z= 0.353 Chirality : 0.052 0.331 1426 Planarity : 0.004 0.046 1410 Dihedral : 11.953 101.429 1918 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.36 % Allowed : 13.57 % 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 are not related in a simple way. whole: 0.74 (0.29), residues: 970 helix: -2.47 (0.81), residues: 24 sheet: 0.81 (0.26), residues: 452 loop : 0.48 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 65 TYR 0.008 0.001 TYR B 121 PHE 0.017 0.002 PHE B 161 TRP 0.008 0.001 TRP C 190 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 8306) covalent geometry : angle 0.70494 / 0.32 (11394) SS BOND : bond 0.00134 / 0.07 ( 2) SS BOND : angle 0.25451 / 0.12 ( 4) hydrogen bonds : bond 0.03508 / 2.36 ( 320) hydrogen bonds : angle 4.44773 / 3.10 ( 1032) link_ALPHA1-3 : bond 0.00815 / 0.47 ( 8) link_ALPHA1-3 : angle 2.43082 / 1.70 ( 24) link_ALPHA1-6 : bond 0.01311 / 0.66 ( 4) link_ALPHA1-6 : angle 1.54973 / 0.87 ( 12) link_BETA1-4 : bond 0.02423 / 1.48 ( 16) link_BETA1-4 : angle 6.07491 / 3.44 ( 48) link_NAG-ASN : bond 0.00208 / 0.14 ( 16) link_NAG-ASN : angle 2.72096 / 1.77 ( 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 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.214 Fit side-chains REVERT: A 147 ASP cc_start: 0.8440 (t0) cc_final: 0.8044 (t0) REVERT: A 269 GLU cc_start: 0.7760 (pp20) cc_final: 0.7262 (pp20) REVERT: B 65 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8389 (ttp-110) REVERT: C 65 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8039 (ttp-110) REVERT: C 67 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8028 (mp0) REVERT: C 112 ASP cc_start: 0.9009 (m-30) cc_final: 0.8647 (p0) REVERT: C 189 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8789 (tt0) REVERT: D 147 ASP cc_start: 0.8453 (t0) cc_final: 0.8083 (t0) REVERT: D 269 GLU cc_start: 0.7821 (pp20) cc_final: 0.7285 (pp20) outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.6836 time to fit residues: 67.1185 Evaluate side-chains 93 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 189 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.063865 restraints weight = 13447.456| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.67 r_work: 0.2613 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3590 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= 0.147 Angle : 0.815 18.195 11530 Z= 0.345 Chirality : 0.051 0.329 1426 Planarity : 0.004 0.045 1410 Dihedral : 11.321 99.418 1918 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.36 % Allowed : 13.81 % Favored : 85.83 % 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: 0.72 (0.29), residues: 970 helix: -2.51 (0.79), residues: 24 sheet: 0.80 (0.26), residues: 449 loop : 0.46 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 65 TYR 0.016 0.001 TYR D 74 PHE 0.017 0.001 PHE B 161 TRP 0.006 0.001 TRP B 190 HIS 0.001 0.000 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8306) covalent geometry : angle 0.68643 / 0.31 (11394) SS BOND : bond 0.00182 / 0.09 ( 2) SS BOND : angle 0.32058 / 0.18 ( 4) hydrogen bonds : bond 0.03205 / 2.16 ( 320) hydrogen bonds : angle 4.34887 / 3.02 ( 1032) link_ALPHA1-3 : bond 0.00844 / 0.49 ( 8) link_ALPHA1-3 : angle 2.31198 / 1.63 ( 24) link_ALPHA1-6 : bond 0.01169 / 0.58 ( 4) link_ALPHA1-6 : angle 2.08054 / 1.12 ( 12) link_BETA1-4 : bond 0.02440 / 1.49 ( 16) link_BETA1-4 : angle 6.05059 / 3.43 ( 48) link_NAG-ASN : bond 0.00123 / 0.08 ( 16) link_NAG-ASN : angle 2.67998 / 1.74 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.10 seconds wall clock time: 39 minutes 46.38 seconds (2386.38 seconds total)