Starting phenix.real_space_refine on Thu Jul 2 07:22:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vby_64936/07_2026/9vby_64936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vby_64936/07_2026/9vby_64936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vby_64936/07_2026/9vby_64936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vby_64936/07_2026/9vby_64936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vby_64936/07_2026/9vby_64936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vby_64936/07_2026/9vby_64936.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 4 7.51 5 C 4696 2.51 5 N 1200 2.21 5 O 1481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 7385 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1806 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "B" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1806 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "C" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1806 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "D" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1806 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "b" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.22 Number of scatterers: 7385 At special positions: 0 Unit cell: (78.85, 87.15, 81.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 4 24.99 Ca 4 19.99 O 1481 8.00 N 1200 7.00 C 4696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-6 " BMA a 1 " - " MAN a 2 " " BMA b 1 " - " MAN b 2 " " BMA c 1 " - " MAN c 2 " " BMA d 1 " - " MAN d 2 " BETA1-2 " MAN a 2 " - " NAG a 3 " " MAN b 2 " - " NAG b 3 " " MAN c 2 " - " NAG c 3 " " MAN d 2 " - " NAG d 3 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 364.5 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 12 sheets defined 5.4% alpha, 56.7% 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 102 through 106 removed outlier: 3.849A pdb=" N PHE A 105 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.827A pdb=" N PHE B 105 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.818A pdb=" N PHE C 105 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.853A pdb=" N PHE D 105 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 210 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.398A pdb=" N ALA A 63 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR A 247 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 65 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 245 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER A 67 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER A 243 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP A 69 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 241 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 71 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP A 239 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 73 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN D 73 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TRP D 239 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE D 71 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE D 241 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP D 69 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER D 243 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER D 67 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU D 245 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU D 65 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 247 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 63 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22 removed outlier: 5.629A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 22 removed outlier: 5.629A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 226 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 87 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 166 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 208 removed outlier: 6.503A pdb=" N ALA B 63 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 247 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 65 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU B 245 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER B 67 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER B 243 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 69 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B 241 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 71 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP B 239 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 73 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN C 73 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP C 239 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 71 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE C 241 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP C 69 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 243 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 67 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU C 245 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU C 65 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 247 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 63 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 5.629A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 22 removed outlier: 5.629A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 87 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 166 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 22 removed outlier: 5.614A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 22 removed outlier: 5.614A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 87 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 166 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 22 removed outlier: 5.631A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 22 removed outlier: 5.631A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 226 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 87 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL D 166 " --> pdb=" O ILE D 157 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1038 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: 1.18 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1180 1.28 - 1.35: 1130 1.35 - 1.42: 892 1.42 - 1.48: 1222 1.48 - 1.55: 3148 Bond restraints: 7572 Sorted by residual: bond pdb=" N TYR B 197 " pdb=" CA TYR B 197 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.11e-02 8.12e+03 9.32e+00 bond pdb=" N TYR C 197 " pdb=" CA TYR C 197 " ideal model delta sigma weight residual 1.452 1.485 -0.033 1.11e-02 8.12e+03 8.69e+00 bond pdb=" N TYR D 197 " pdb=" CA TYR D 197 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.11e-02 8.12e+03 8.46e+00 bond pdb=" N TYR A 197 " pdb=" CA TYR A 197 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.11e-02 8.12e+03 8.42e+00 bond pdb=" N SER D 44 " pdb=" CA SER D 44 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.01e+00 ... (remaining 7567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 10199 2.67 - 5.34: 140 5.34 - 8.02: 17 8.02 - 10.69: 0 10.69 - 13.36: 4 Bond angle restraints: 10360 Sorted by residual: angle pdb=" C6 NAG a 3 " pdb=" C5 NAG a 3 " pdb=" O5 NAG a 3 " ideal model delta sigma weight residual 108.73 122.09 -13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" C6 NAG b 3 " pdb=" C5 NAG b 3 " pdb=" O5 NAG b 3 " ideal model delta sigma weight residual 108.73 122.07 -13.34 3.00e+00 1.11e-01 1.98e+01 angle pdb=" C6 NAG c 3 " pdb=" C5 NAG c 3 " pdb=" O5 NAG c 3 " ideal model delta sigma weight residual 108.73 122.06 -13.33 3.00e+00 1.11e-01 1.98e+01 angle pdb=" C6 NAG d 3 " pdb=" C5 NAG d 3 " pdb=" O5 NAG d 3 " ideal model delta sigma weight residual 108.73 122.02 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CA ALA C 112 " pdb=" C ALA C 112 " pdb=" O ALA C 112 " ideal model delta sigma weight residual 122.14 118.32 3.82 1.24e+00 6.50e-01 9.48e+00 ... (remaining 10355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 4003 21.02 - 42.05: 428 42.05 - 63.07: 73 63.07 - 84.09: 28 84.09 - 105.11: 16 Dihedral angle restraints: 4548 sinusoidal: 1848 harmonic: 2700 Sorted by residual: dihedral pdb=" O4 BMA d 1 " pdb=" C4 BMA d 1 " pdb=" C5 BMA d 1 " pdb=" O5 BMA d 1 " ideal model delta sinusoidal sigma weight residual -71.29 -176.40 105.11 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" O4 BMA b 1 " pdb=" C4 BMA b 1 " pdb=" C5 BMA b 1 " pdb=" O5 BMA b 1 " ideal model delta sinusoidal sigma weight residual -71.29 -176.40 105.11 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" O4 BMA c 1 " pdb=" C4 BMA c 1 " pdb=" C5 BMA c 1 " pdb=" O5 BMA c 1 " ideal model delta sinusoidal sigma weight residual -71.29 -176.38 105.09 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 4545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 1180 0.188 - 0.375: 16 0.375 - 0.562: 8 0.562 - 0.750: 0 0.750 - 0.937: 4 Chirality restraints: 1208 Sorted by residual: chirality pdb=" C1 MAN d 2 " pdb=" O6 BMA d 1 " pdb=" C2 MAN d 2 " pdb=" O5 MAN d 2 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.20e+03 chirality pdb=" C1 MAN c 2 " pdb=" O6 BMA c 1 " pdb=" C2 MAN c 2 " pdb=" O5 MAN c 2 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.19e+03 chirality pdb=" C1 MAN a 2 " pdb=" O6 BMA a 1 " pdb=" C2 MAN a 2 " pdb=" O5 MAN a 2 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.19e+03 ... (remaining 1205 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 3 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG d 3 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG d 3 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG d 3 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG d 3 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 3 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG b 3 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG b 3 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG b 3 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG b 3 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 3 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG c 3 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG c 3 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG c 3 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG c 3 " -0.008 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 84 2.57 - 3.16: 5652 3.16 - 3.74: 12175 3.74 - 4.32: 17927 4.32 - 4.90: 29751 Nonbonded interactions: 65589 Sorted by model distance: nonbonded pdb=" O3 MAN c 2 " pdb=" O HOH C 401 " model vdw 1.993 3.040 nonbonded pdb=" O5 BMA d 1 " pdb=" O HOH D 401 " model vdw 2.076 3.040 nonbonded pdb=" NE2 GLN D 229 " pdb=" O1 BMA d 1 " model vdw 2.097 3.120 nonbonded pdb=" C6 BMA d 1 " pdb=" O HOH D 401 " model vdw 2.147 3.440 nonbonded pdb=" OD2 ASP C 140 " pdb="MN MN C 302 " model vdw 2.216 3.060 ... (remaining 65584 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.110 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.860 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.008 0.256 7580 Z= 0.453 Angle : 1.015 22.641 10384 Z= 0.484 Chirality : 0.085 0.937 1208 Planarity : 0.004 0.036 1300 Dihedral : 19.018 105.113 2804 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.36 % Allowed : 27.23 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.25 (0.25), residues: 908 helix: None (None), residues: 0 sheet: 1.06 (0.26), residues: 360 loop : -1.08 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 57 TYR 0.007 0.001 TYR B 196 PHE 0.008 0.001 PHE B 241 TRP 0.009 0.001 TRP B 172 HIS 0.003 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.30 ( 7572) covalent geometry : angle 0.79421 / 0.44 (10360) hydrogen bonds : bond 0.23522 / 15.28 ( 322) hydrogen bonds : angle 8.67809 / 6.27 ( 1038) link_ALPHA1-6 : bond 0.25612 / 11.77 ( 4) link_ALPHA1-6 : angle 14.05469 / 8.84 ( 12) link_BETA1-2 : bond 0.15235 / 7.01 ( 4) link_BETA1-2 : angle 12.22339 / 7.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.265 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 201 average time/residue: 0.3913 time to fit residues: 84.4468 Evaluate side-chains 180 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.167613 restraints weight = 7103.533| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.65 r_work: 0.3799 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7580 Z= 0.144 Angle : 0.618 5.241 10384 Z= 0.328 Chirality : 0.047 0.175 1208 Planarity : 0.004 0.028 1300 Dihedral : 12.763 75.416 1234 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.58 % Allowed : 23.39 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.04 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 1.14 (0.27), residues: 344 loop : -0.83 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.009 0.001 TYR A 101 PHE 0.015 0.002 PHE A 68 TRP 0.006 0.001 TRP B 172 HIS 0.004 0.001 HIS D 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7572) covalent geometry : angle 0.61115 / 0.33 (10360) hydrogen bonds : bond 0.04821 / 3.14 ( 322) hydrogen bonds : angle 5.77430 / 4.09 ( 1038) link_ALPHA1-6 : bond 0.00425 / 0.19 ( 4) link_ALPHA1-6 : angle 1.32422 / 0.84 ( 12) link_BETA1-2 : bond 0.00156 / 0.07 ( 4) link_BETA1-2 : angle 2.42545 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.226 Fit side-chains REVERT: A 169 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: D 35 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7946 (ttpp) outliers start: 37 outliers final: 18 residues processed: 209 average time/residue: 0.3319 time to fit residues: 74.9755 Evaluate side-chains 203 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 231 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN A 248 ASN B 234 ASN B 248 ASN C 234 ASN C 248 ASN D 234 ASN D 248 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164614 restraints weight = 7071.024| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.61 r_work: 0.3758 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7580 Z= 0.241 Angle : 0.654 7.513 10384 Z= 0.349 Chirality : 0.048 0.146 1208 Planarity : 0.004 0.034 1300 Dihedral : 11.125 61.876 1232 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.94 % Allowed : 22.90 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.14 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 1.09 (0.28), residues: 344 loop : -0.91 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.009 0.002 TYR C 147 PHE 0.016 0.003 PHE A 68 TRP 0.007 0.002 TRP B 170 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.24 ( 7572) covalent geometry : angle 0.64750 / 0.35 (10360) hydrogen bonds : bond 0.05131 / 3.35 ( 322) hydrogen bonds : angle 5.65588 / 4.02 ( 1038) link_ALPHA1-6 : bond 0.00437 / 0.20 ( 4) link_ALPHA1-6 : angle 1.50214 / 0.98 ( 12) link_BETA1-2 : bond 0.00134 / 0.06 ( 4) link_BETA1-2 : angle 2.37230 / 1.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.305 Fit side-chains REVERT: A 28 ASN cc_start: 0.7233 (p0) cc_final: 0.6998 (p0) REVERT: A 169 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8143 (ttpp) REVERT: B 101 TYR cc_start: 0.7195 (t80) cc_final: 0.6881 (t80) REVERT: B 233 ARG cc_start: 0.8126 (mpp80) cc_final: 0.7919 (mtm-85) REVERT: C 101 TYR cc_start: 0.7214 (t80) cc_final: 0.6903 (t80) REVERT: C 169 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: D 138 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: D 169 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8179 (ttpp) outliers start: 48 outliers final: 32 residues processed: 198 average time/residue: 0.3158 time to fit residues: 67.5534 Evaluate side-chains 194 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 230 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 234 ASN B 248 ASN C 234 ASN D 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.192350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163705 restraints weight = 7172.661| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.66 r_work: 0.3773 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7580 Z= 0.205 Angle : 0.631 6.335 10384 Z= 0.336 Chirality : 0.048 0.164 1208 Planarity : 0.004 0.031 1300 Dihedral : 8.904 44.671 1232 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 6.19 % Allowed : 22.65 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.25 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.94 (0.28), residues: 344 loop : -0.93 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 57 TYR 0.013 0.002 TYR C 142 PHE 0.014 0.002 PHE C 68 TRP 0.005 0.001 TRP B 59 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 7572) covalent geometry : angle 0.62616 / 0.34 (10360) hydrogen bonds : bond 0.04562 / 2.99 ( 322) hydrogen bonds : angle 5.44970 / 3.87 ( 1038) link_ALPHA1-6 : bond 0.00291 / 0.13 ( 4) link_ALPHA1-6 : angle 1.46796 / 0.94 ( 12) link_BETA1-2 : bond 0.00249 / 0.11 ( 4) link_BETA1-2 : angle 2.09027 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.220 Fit side-chains REVERT: A 10 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8481 (ptpp) REVERT: A 69 ASP cc_start: 0.8021 (t70) cc_final: 0.7740 (t70) REVERT: A 101 TYR cc_start: 0.7201 (t80) cc_final: 0.6810 (t80) REVERT: A 158 ASP cc_start: 0.7845 (m-30) cc_final: 0.7540 (m-30) REVERT: A 169 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (ttpp) REVERT: B 28 ASN cc_start: 0.7149 (p0) cc_final: 0.6939 (p0) REVERT: B 101 TYR cc_start: 0.7126 (t80) cc_final: 0.6909 (t80) REVERT: B 169 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8161 (ttpp) REVERT: C 28 ASN cc_start: 0.7173 (p0) cc_final: 0.6946 (p0) REVERT: C 69 ASP cc_start: 0.7866 (t70) cc_final: 0.7616 (t70) REVERT: C 169 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8169 (ttpp) REVERT: D 101 TYR cc_start: 0.7139 (t80) cc_final: 0.6777 (t80) REVERT: D 169 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8170 (ttpp) outliers start: 50 outliers final: 28 residues processed: 203 average time/residue: 0.2922 time to fit residues: 64.0194 Evaluate side-chains 194 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 231 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 234 ASN C 111 ASN C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.197510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169451 restraints weight = 7178.303| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.66 r_work: 0.3825 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7580 Z= 0.113 Angle : 0.558 6.274 10384 Z= 0.297 Chirality : 0.046 0.144 1208 Planarity : 0.003 0.032 1300 Dihedral : 7.286 48.295 1232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 5.94 % Allowed : 23.39 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.28 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.83 (0.27), residues: 344 loop : -0.88 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 57 TYR 0.009 0.001 TYR D 207 PHE 0.013 0.002 PHE B 68 TRP 0.005 0.001 TRP A 59 HIS 0.005 0.001 HIS D 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 7572) covalent geometry : angle 0.55366 / 0.30 (10360) hydrogen bonds : bond 0.03672 / 2.42 ( 322) hydrogen bonds : angle 4.97828 / 3.50 ( 1038) link_ALPHA1-6 : bond 0.00315 / 0.16 ( 4) link_ALPHA1-6 : angle 1.55922 / 1.02 ( 12) link_BETA1-2 : bond 0.00296 / 0.14 ( 4) link_BETA1-2 : angle 1.62722 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.273 Fit side-chains REVERT: A 101 TYR cc_start: 0.7109 (t80) cc_final: 0.6741 (t80) REVERT: A 169 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8169 (ttpp) REVERT: B 101 TYR cc_start: 0.6784 (t80) cc_final: 0.6519 (t80) REVERT: B 169 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8133 (ttpp) REVERT: C 69 ASP cc_start: 0.7841 (t70) cc_final: 0.7619 (t70) REVERT: D 28 ASN cc_start: 0.7103 (p0) cc_final: 0.6898 (p0) REVERT: D 69 ASP cc_start: 0.7867 (t70) cc_final: 0.7614 (t70) REVERT: D 101 TYR cc_start: 0.7030 (t80) cc_final: 0.6653 (t80) REVERT: D 169 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8190 (ttpp) outliers start: 48 outliers final: 19 residues processed: 212 average time/residue: 0.3328 time to fit residues: 76.1113 Evaluate side-chains 191 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN A 248 ASN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 248 ASN D 248 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.195538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167992 restraints weight = 7185.435| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.59 r_work: 0.3761 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7580 Z= 0.168 Angle : 0.594 6.768 10384 Z= 0.316 Chirality : 0.046 0.148 1208 Planarity : 0.004 0.034 1300 Dihedral : 7.155 49.647 1232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.94 % Allowed : 22.90 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.31 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.84 (0.27), residues: 344 loop : -0.92 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 57 TYR 0.009 0.001 TYR D 147 PHE 0.015 0.002 PHE D 68 TRP 0.005 0.001 TRP A 59 HIS 0.007 0.001 HIS D 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7572) covalent geometry : angle 0.58803 / 0.31 (10360) hydrogen bonds : bond 0.04103 / 2.71 ( 322) hydrogen bonds : angle 5.05314 / 3.57 ( 1038) link_ALPHA1-6 : bond 0.00356 / 0.15 ( 4) link_ALPHA1-6 : angle 1.37404 / 0.89 ( 12) link_BETA1-2 : bond 0.00170 / 0.08 ( 4) link_BETA1-2 : angle 2.23098 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.193 Fit side-chains REVERT: A 10 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8523 (ptpp) REVERT: A 101 TYR cc_start: 0.7208 (t80) cc_final: 0.6846 (t80) REVERT: A 169 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: B 101 TYR cc_start: 0.6884 (t80) cc_final: 0.6614 (t80) REVERT: B 169 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8165 (ttpp) REVERT: C 101 TYR cc_start: 0.7111 (t80) cc_final: 0.6739 (t80) REVERT: C 169 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (ttpp) REVERT: D 69 ASP cc_start: 0.8076 (t70) cc_final: 0.7793 (t70) REVERT: D 101 TYR cc_start: 0.7154 (t80) cc_final: 0.6805 (t80) REVERT: D 169 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8233 (ttpp) outliers start: 48 outliers final: 29 residues processed: 210 average time/residue: 0.3040 time to fit residues: 69.0245 Evaluate side-chains 211 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 111 ASN B 234 ASN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160027 restraints weight = 7121.111| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.62 r_work: 0.3716 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7580 Z= 0.175 Angle : 0.594 6.193 10384 Z= 0.320 Chirality : 0.046 0.144 1208 Planarity : 0.004 0.033 1300 Dihedral : 6.995 47.810 1232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.82 % Allowed : 24.01 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.33 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.83 (0.27), residues: 344 loop : -0.94 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.018 0.001 TYR B 147 PHE 0.014 0.002 PHE B 68 TRP 0.004 0.001 TRP C 59 HIS 0.009 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7572) covalent geometry : angle 0.58947 / 0.32 (10360) hydrogen bonds : bond 0.04119 / 2.73 ( 322) hydrogen bonds : angle 5.03613 / 3.56 ( 1038) link_ALPHA1-6 : bond 0.00330 / 0.15 ( 4) link_ALPHA1-6 : angle 1.38323 / 0.89 ( 12) link_BETA1-2 : bond 0.00164 / 0.08 ( 4) link_BETA1-2 : angle 1.91941 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.189 Fit side-chains REVERT: A 10 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (ptpp) REVERT: A 101 TYR cc_start: 0.7173 (t80) cc_final: 0.6843 (t80) REVERT: A 169 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8188 (ttpp) REVERT: B 101 TYR cc_start: 0.6887 (t80) cc_final: 0.6658 (t80) REVERT: B 169 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: B 217 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8157 (mt-10) REVERT: C 101 TYR cc_start: 0.7008 (t80) cc_final: 0.6632 (t80) REVERT: C 169 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8206 (ttpp) REVERT: D 101 TYR cc_start: 0.7101 (t80) cc_final: 0.6713 (t80) REVERT: D 169 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8206 (ttpp) outliers start: 47 outliers final: 25 residues processed: 209 average time/residue: 0.3729 time to fit residues: 83.8929 Evaluate side-chains 216 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 ASN B 234 ASN D 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.192397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163200 restraints weight = 7096.696| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.65 r_work: 0.3742 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7580 Z= 0.130 Angle : 0.568 6.552 10384 Z= 0.305 Chirality : 0.045 0.157 1208 Planarity : 0.004 0.033 1300 Dihedral : 6.606 45.707 1232 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.70 % Allowed : 25.50 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.35 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.80 (0.27), residues: 344 loop : -0.94 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 57 TYR 0.008 0.001 TYR C 147 PHE 0.013 0.002 PHE D 68 TRP 0.003 0.001 TRP A 59 HIS 0.008 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 7572) covalent geometry : angle 0.56485 / 0.30 (10360) hydrogen bonds : bond 0.03739 / 2.48 ( 322) hydrogen bonds : angle 4.83167 / 3.41 ( 1038) link_ALPHA1-6 : bond 0.00337 / 0.15 ( 4) link_ALPHA1-6 : angle 1.44785 / 0.92 ( 12) link_BETA1-2 : bond 0.00268 / 0.13 ( 4) link_BETA1-2 : angle 1.38686 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.290 Fit side-chains REVERT: A 10 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8491 (ptpp) REVERT: A 101 TYR cc_start: 0.7062 (t80) cc_final: 0.6676 (t80) REVERT: A 169 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8234 (ttpp) REVERT: B 101 TYR cc_start: 0.6723 (t80) cc_final: 0.6474 (t80) REVERT: B 111 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.6164 (m110) REVERT: B 169 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: C 101 TYR cc_start: 0.6846 (t80) cc_final: 0.6465 (t80) REVERT: D 69 ASP cc_start: 0.8011 (t70) cc_final: 0.7725 (t70) REVERT: D 101 TYR cc_start: 0.6967 (t80) cc_final: 0.6609 (t80) REVERT: D 169 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8215 (ttpp) outliers start: 38 outliers final: 21 residues processed: 205 average time/residue: 0.3840 time to fit residues: 84.6152 Evaluate side-chains 205 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN B 111 ASN B 234 ASN C 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.193129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.165627 restraints weight = 7195.329| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.58 r_work: 0.3730 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7580 Z= 0.240 Angle : 0.647 7.282 10384 Z= 0.350 Chirality : 0.048 0.170 1208 Planarity : 0.004 0.034 1300 Dihedral : 6.999 46.899 1232 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.33 % Allowed : 26.24 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.36 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.84 (0.28), residues: 336 loop : -0.95 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 49 TYR 0.018 0.002 TYR C 142 PHE 0.017 0.003 PHE C 68 TRP 0.006 0.002 TRP D 170 HIS 0.010 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 ( 7572) covalent geometry : angle 0.64357 / 0.35 (10360) hydrogen bonds : bond 0.04505 / 2.98 ( 322) hydrogen bonds : angle 5.15983 / 3.66 ( 1038) link_ALPHA1-6 : bond 0.00261 / 0.11 ( 4) link_ALPHA1-6 : angle 1.34311 / 0.86 ( 12) link_BETA1-2 : bond 0.00086 / 0.04 ( 4) link_BETA1-2 : angle 1.84592 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.230 Fit side-chains REVERT: A 10 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8532 (ptpp) REVERT: A 101 TYR cc_start: 0.7257 (t80) cc_final: 0.6933 (t80) REVERT: A 169 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8226 (ttpp) REVERT: B 101 TYR cc_start: 0.6988 (t80) cc_final: 0.6714 (t80) REVERT: B 169 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8184 (ttpp) REVERT: C 101 TYR cc_start: 0.7070 (t80) cc_final: 0.6674 (t80) REVERT: D 101 TYR cc_start: 0.7252 (t80) cc_final: 0.6916 (t80) REVERT: D 169 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8216 (ttpp) outliers start: 35 outliers final: 24 residues processed: 188 average time/residue: 0.4069 time to fit residues: 81.9862 Evaluate side-chains 195 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN B 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.196968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169771 restraints weight = 7271.052| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.59 r_work: 0.3812 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7580 Z= 0.134 Angle : 0.578 6.713 10384 Z= 0.313 Chirality : 0.046 0.171 1208 Planarity : 0.004 0.033 1300 Dihedral : 6.631 47.896 1232 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.84 % Allowed : 26.49 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.39 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.96 (0.27), residues: 336 loop : -1.08 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.016 0.001 TYR B 142 PHE 0.013 0.002 PHE B 68 TRP 0.004 0.001 TRP C 59 HIS 0.010 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7572) covalent geometry : angle 0.57472 / 0.31 (10360) hydrogen bonds : bond 0.03772 / 2.50 ( 322) hydrogen bonds : angle 4.85897 / 3.43 ( 1038) link_ALPHA1-6 : bond 0.00269 / 0.12 ( 4) link_ALPHA1-6 : angle 1.45107 / 0.92 ( 12) link_BETA1-2 : bond 0.00208 / 0.10 ( 4) link_BETA1-2 : angle 1.37543 / 0.85 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.222 Fit side-chains REVERT: A 69 ASP cc_start: 0.8066 (t70) cc_final: 0.7793 (t70) REVERT: A 101 TYR cc_start: 0.7164 (t80) cc_final: 0.6817 (t80) REVERT: A 169 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8253 (ttpp) REVERT: B 169 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8254 (ttpp) REVERT: C 101 TYR cc_start: 0.6978 (t80) cc_final: 0.6575 (t80) REVERT: C 169 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8203 (ttpp) REVERT: D 101 TYR cc_start: 0.7110 (t80) cc_final: 0.6766 (t80) outliers start: 31 outliers final: 21 residues processed: 197 average time/residue: 0.3590 time to fit residues: 75.9755 Evaluate side-chains 196 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 0.0040 chunk 82 optimal weight: 0.4980 overall best weight: 1.1134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 ASN B 234 ASN B 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.169340 restraints weight = 7194.181| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.58 r_work: 0.3800 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7580 Z= 0.150 Angle : 0.593 6.573 10384 Z= 0.321 Chirality : 0.046 0.170 1208 Planarity : 0.004 0.034 1300 Dihedral : 6.590 47.717 1232 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.59 % Allowed : 26.49 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.40 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.77 (0.28), residues: 336 loop : -0.96 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.021 0.001 TYR C 142 PHE 0.015 0.002 PHE B 68 TRP 0.004 0.001 TRP A 59 HIS 0.003 0.001 HIS D 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 7572) covalent geometry : angle 0.58968 / 0.32 (10360) hydrogen bonds : bond 0.03943 / 2.62 ( 322) hydrogen bonds : angle 4.86120 / 3.44 ( 1038) link_ALPHA1-6 : bond 0.00296 / 0.14 ( 4) link_ALPHA1-6 : angle 1.38870 / 0.86 ( 12) link_BETA1-2 : bond 0.00197 / 0.09 ( 4) link_BETA1-2 : angle 1.58681 / 1.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.46 seconds wall clock time: 43 minutes 55.89 seconds (2635.89 seconds total)