Starting phenix.real_space_refine on Sun Apr 5 02:32:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vby_64936/04_2026/9vby_64936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vby_64936/04_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_64936/04_2026/9vby_64936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vby_64936/04_2026/9vby_64936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vby_64936/04_2026/9vby_64936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vby_64936/04_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 1.62, 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: 0.74 Conformation dependent library (CDL) restraints added in 226.9 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: 0.31 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: 0.93 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 2.320 ... (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: 1.060 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: 8.220 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 covalent geometry : bond 0.00481 ( 7572) covalent geometry : angle 0.79421 (10360) hydrogen bonds : bond 0.23522 ( 322) hydrogen bonds : angle 8.67809 ( 1038) link_ALPHA1-6 : bond 0.25612 ( 4) link_ALPHA1-6 : angle 14.05469 ( 12) link_BETA1-2 : bond 0.15235 ( 4) link_BETA1-2 : angle 12.22339 ( 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 : 0.243 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 201 average time/residue: 0.4341 time to fit residues: 93.2030 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 : 0.212 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4216 r_free = 0.4216 target = 0.194767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166426 restraints weight = 7275.513| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.69 r_work: 0.3787 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7580 Z= 0.146 Angle : 0.607 5.256 10384 Z= 0.325 Chirality : 0.046 0.149 1208 Planarity : 0.004 0.029 1300 Dihedral : 13.115 77.504 1234 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.21 % Allowed : 23.76 % 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: -0.03 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 1.15 (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 D 57 TYR 0.010 0.001 TYR A 101 PHE 0.014 0.002 PHE A 68 TRP 0.005 0.001 TRP B 172 HIS 0.004 0.001 HIS D 212 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7572) covalent geometry : angle 0.60029 (10360) hydrogen bonds : bond 0.05250 ( 322) hydrogen bonds : angle 5.88260 ( 1038) link_ALPHA1-6 : bond 0.00591 ( 4) link_ALPHA1-6 : angle 1.57490 ( 12) link_BETA1-2 : bond 0.00203 ( 4) link_BETA1-2 : angle 2.27669 ( 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 227 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.299 Fit side-chains REVERT: A 169 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8151 (ttpp) outliers start: 34 outliers final: 20 residues processed: 209 average time/residue: 0.3838 time to fit residues: 86.4244 Evaluate side-chains 209 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 A residue 231 LYS 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 35 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LYS 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: 0.3980 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 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: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4217 r_free = 0.4217 target = 0.194697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167229 restraints weight = 7251.673| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.63 r_work: 0.3790 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1410 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= 0.167 Angle : 0.596 5.916 10384 Z= 0.318 Chirality : 0.047 0.165 1208 Planarity : 0.004 0.034 1300 Dihedral : 10.834 61.101 1232 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.07 % Allowed : 24.13 % Favored : 70.79 % 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: -0.11 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 1.05 (0.27), residues: 344 loop : -0.84 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 49 TYR 0.009 0.001 TYR D 207 PHE 0.015 0.002 PHE B 68 TRP 0.006 0.001 TRP D 59 HIS 0.005 0.001 HIS D 212 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7572) covalent geometry : angle 0.58946 (10360) hydrogen bonds : bond 0.04718 ( 322) hydrogen bonds : angle 5.47663 ( 1038) link_ALPHA1-6 : bond 0.00374 ( 4) link_ALPHA1-6 : angle 1.54390 ( 12) link_BETA1-2 : bond 0.00152 ( 4) link_BETA1-2 : angle 2.27084 ( 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 233 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.222 Fit side-chains REVERT: A 28 ASN cc_start: 0.7203 (p0) cc_final: 0.6929 (p0) REVERT: A 169 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: B 101 TYR cc_start: 0.7133 (t80) cc_final: 0.6805 (t80) REVERT: C 101 TYR cc_start: 0.7103 (t80) cc_final: 0.6785 (t80) REVERT: C 169 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8157 (ttpp) REVERT: D 35 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7915 (ttpp) REVERT: D 169 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8170 (ttpp) outliers start: 41 outliers final: 29 residues processed: 207 average time/residue: 0.3898 time to fit residues: 86.7705 Evaluate side-chains 211 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 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 97 SER 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 97 SER 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 97 SER 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: 8.9990 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN B 234 ASN C 234 ASN D 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.194298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166716 restraints weight = 7362.496| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.62 r_work: 0.3785 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1594 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= 0.173 Angle : 0.593 5.871 10384 Z= 0.317 Chirality : 0.047 0.165 1208 Planarity : 0.004 0.034 1300 Dihedral : 8.493 46.650 1232 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 5.45 % Allowed : 23.39 % 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: -0.19 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.95 (0.27), residues: 344 loop : -0.85 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 57 TYR 0.012 0.001 TYR B 142 PHE 0.014 0.002 PHE A 68 TRP 0.005 0.001 TRP A 59 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7572) covalent geometry : angle 0.58751 (10360) hydrogen bonds : bond 0.04343 ( 322) hydrogen bonds : angle 5.29858 ( 1038) link_ALPHA1-6 : bond 0.00341 ( 4) link_ALPHA1-6 : angle 1.53140 ( 12) link_BETA1-2 : bond 0.00195 ( 4) link_BETA1-2 : angle 1.90039 ( 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 241 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.319 Fit side-chains REVERT: A 169 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8194 (ttpp) REVERT: B 28 ASN cc_start: 0.7117 (p0) cc_final: 0.6901 (p0) REVERT: B 101 TYR cc_start: 0.7073 (t80) cc_final: 0.6851 (t80) REVERT: B 169 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8211 (ttpp) REVERT: C 28 ASN cc_start: 0.7167 (p0) cc_final: 0.6910 (p0) REVERT: C 101 TYR cc_start: 0.7040 (t80) cc_final: 0.6744 (t80) REVERT: C 169 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8248 (ttpp) REVERT: C 217 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 28 ASN cc_start: 0.7110 (p0) cc_final: 0.6904 (p0) REVERT: D 101 TYR cc_start: 0.7149 (t80) cc_final: 0.6925 (t80) REVERT: D 169 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8211 (ttpp) outliers start: 44 outliers final: 29 residues processed: 215 average time/residue: 0.3747 time to fit residues: 86.7321 Evaluate side-chains 209 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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 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 108 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.0470 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 248 ASN B 234 ASN B 248 ASN C 234 ASN D 248 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162306 restraints weight = 6893.197| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.61 r_work: 0.3726 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7580 Z= 0.144 Angle : 0.563 5.229 10384 Z= 0.304 Chirality : 0.046 0.141 1208 Planarity : 0.004 0.033 1300 Dihedral : 7.253 49.457 1232 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 6.19 % Allowed : 22.90 % Favored : 70.92 % 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: -0.22 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.84 (0.28), residues: 336 loop : -0.78 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.011 0.001 TYR D 142 PHE 0.014 0.002 PHE B 68 TRP 0.004 0.001 TRP D 59 HIS 0.007 0.001 HIS D 212 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7572) covalent geometry : angle 0.55871 (10360) hydrogen bonds : bond 0.03988 ( 322) hydrogen bonds : angle 5.07532 ( 1038) link_ALPHA1-6 : bond 0.00319 ( 4) link_ALPHA1-6 : angle 1.51519 ( 12) link_BETA1-2 : bond 0.00220 ( 4) link_BETA1-2 : angle 1.62767 ( 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 224 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.174 Fit side-chains REVERT: A 10 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8469 (ptpp) REVERT: A 101 TYR cc_start: 0.6958 (t80) cc_final: 0.6616 (t80) REVERT: A 169 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8194 (ttpp) REVERT: B 101 TYR cc_start: 0.6837 (t80) cc_final: 0.6519 (t80) REVERT: C 101 TYR cc_start: 0.6901 (t80) cc_final: 0.6611 (t80) REVERT: C 169 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8240 (ttpp) REVERT: C 217 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 28 ASN cc_start: 0.7179 (p0) cc_final: 0.6937 (p0) REVERT: D 69 ASP cc_start: 0.8039 (t70) cc_final: 0.7775 (t70) REVERT: D 111 ASN cc_start: 0.6413 (OUTLIER) cc_final: 0.6054 (t0) REVERT: D 169 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8198 (ttpp) outliers start: 50 outliers final: 29 residues processed: 199 average time/residue: 0.3980 time to fit residues: 85.0442 Evaluate side-chains 215 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 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 99 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4217 r_free = 0.4217 target = 0.194672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167839 restraints weight = 7271.150| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.53 r_work: 0.3755 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1890 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 : 0.614 6.639 10384 Z= 0.331 Chirality : 0.047 0.142 1208 Planarity : 0.004 0.033 1300 Dihedral : 7.289 49.714 1232 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 5.69 % Allowed : 23.39 % Favored : 70.92 % 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: -0.29 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.86 (0.28), residues: 336 loop : -0.89 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.009 0.001 TYR C 52 PHE 0.016 0.002 PHE B 68 TRP 0.005 0.001 TRP D 170 HIS 0.006 0.001 HIS D 212 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7572) covalent geometry : angle 0.60868 (10360) hydrogen bonds : bond 0.04411 ( 322) hydrogen bonds : angle 5.24317 ( 1038) link_ALPHA1-6 : bond 0.00237 ( 4) link_ALPHA1-6 : angle 1.41574 ( 12) link_BETA1-2 : bond 0.00150 ( 4) link_BETA1-2 : angle 2.07150 ( 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 234 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 0.233 Fit side-chains REVERT: A 10 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8515 (ptpp) REVERT: A 169 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8219 (ttpp) REVERT: B 101 TYR cc_start: 0.7004 (t80) cc_final: 0.6697 (t80) REVERT: B 217 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8154 (mt-10) REVERT: C 101 TYR cc_start: 0.6946 (t80) cc_final: 0.6700 (t80) REVERT: C 169 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8253 (ttpp) REVERT: D 101 TYR cc_start: 0.7136 (t80) cc_final: 0.6876 (t80) REVERT: D 169 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8210 (ttpp) outliers start: 46 outliers final: 30 residues processed: 211 average time/residue: 0.3830 time to fit residues: 87.0160 Evaluate side-chains 220 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 56 LEU 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 230 ASP 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 99 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 193 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN B 111 ASN B 234 ASN C 111 ASN C 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168457 restraints weight = 7221.082| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.52 r_work: 0.3779 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7580 Z= 0.175 Angle : 0.595 5.956 10384 Z= 0.323 Chirality : 0.046 0.156 1208 Planarity : 0.004 0.032 1300 Dihedral : 7.029 47.615 1232 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.20 % Allowed : 23.27 % Favored : 71.53 % 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 (0.28), residues: 336 loop : -0.91 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.009 0.001 TYR D 142 PHE 0.014 0.002 PHE B 68 TRP 0.004 0.001 TRP C 170 HIS 0.008 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7572) covalent geometry : angle 0.59134 (10360) hydrogen bonds : bond 0.04200 ( 322) hydrogen bonds : angle 5.11734 ( 1038) link_ALPHA1-6 : bond 0.00315 ( 4) link_ALPHA1-6 : angle 1.36038 ( 12) link_BETA1-2 : bond 0.00174 ( 4) link_BETA1-2 : angle 1.70752 ( 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 230 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.175 Fit side-chains REVERT: A 10 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8536 (ptpp) REVERT: A 69 ASP cc_start: 0.8158 (t70) cc_final: 0.7889 (t70) REVERT: A 101 TYR cc_start: 0.7236 (t80) cc_final: 0.6866 (t80) REVERT: A 169 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8234 (ttpp) REVERT: B 101 TYR cc_start: 0.7019 (t80) cc_final: 0.6809 (t80) REVERT: B 169 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8227 (ttpp) REVERT: C 101 TYR cc_start: 0.6898 (t80) cc_final: 0.6645 (t80) REVERT: C 169 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8245 (ttpp) REVERT: D 101 TYR cc_start: 0.7099 (t80) cc_final: 0.6863 (t80) REVERT: D 169 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8252 (ttpp) outliers start: 42 outliers final: 27 residues processed: 207 average time/residue: 0.3958 time to fit residues: 88.0714 Evaluate side-chains 209 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 56 LEU 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 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 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 193 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 35 LYS 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: 5.9990 chunk 78 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 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 = 0.4255 r_free = 0.4255 target = 0.198360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172094 restraints weight = 7344.688| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.53 r_work: 0.3837 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7580 Z= 0.123 Angle : 0.566 6.825 10384 Z= 0.304 Chirality : 0.045 0.162 1208 Planarity : 0.004 0.033 1300 Dihedral : 6.541 44.995 1232 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.46 % Allowed : 23.89 % Favored : 71.66 % 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: 0.79 (0.26), residues: 356 loop : -0.94 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.013 0.001 TYR A 147 PHE 0.013 0.002 PHE A 68 TRP 0.003 0.001 TRP A 59 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7572) covalent geometry : angle 0.56235 (10360) hydrogen bonds : bond 0.03669 ( 322) hydrogen bonds : angle 4.83967 ( 1038) link_ALPHA1-6 : bond 0.00288 ( 4) link_ALPHA1-6 : angle 1.47274 ( 12) link_BETA1-2 : bond 0.00287 ( 4) link_BETA1-2 : angle 1.25571 ( 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 220 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.228 Fit side-chains REVERT: A 10 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8507 (ptpp) REVERT: A 101 TYR cc_start: 0.7110 (t80) cc_final: 0.6783 (t80) REVERT: A 169 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8258 (ttpp) REVERT: A 233 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7862 (mtm-85) REVERT: B 138 GLU cc_start: 0.8573 (pt0) cc_final: 0.8359 (pt0) REVERT: D 101 TYR cc_start: 0.7060 (t80) cc_final: 0.6843 (t80) outliers start: 36 outliers final: 19 residues processed: 203 average time/residue: 0.4073 time to fit residues: 88.7717 Evaluate side-chains 199 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 A residue 183 SER Chi-restraints excluded: chain A residue 233 ARG 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 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 231 LYS Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 108 LEU 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: 0.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 234 ASN B 248 ASN C 111 ASN C 248 ASN D 248 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.194667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167520 restraints weight = 7154.904| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.56 r_work: 0.3802 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7580 Z= 0.183 Angle : 0.608 7.168 10384 Z= 0.327 Chirality : 0.047 0.167 1208 Planarity : 0.004 0.034 1300 Dihedral : 6.711 42.765 1232 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.59 % Allowed : 25.00 % 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: -0.31 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.85 (0.27), residues: 356 loop : -0.97 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.019 0.001 TYR B 142 PHE 0.016 0.002 PHE B 68 TRP 0.005 0.001 TRP A 59 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7572) covalent geometry : angle 0.60381 (10360) hydrogen bonds : bond 0.04182 ( 322) hydrogen bonds : angle 5.04529 ( 1038) link_ALPHA1-6 : bond 0.00409 ( 4) link_ALPHA1-6 : angle 1.33874 ( 12) link_BETA1-2 : bond 0.00176 ( 4) link_BETA1-2 : angle 1.83088 ( 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 219 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.325 Fit side-chains REVERT: A 10 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8587 (ptpp) REVERT: A 69 ASP cc_start: 0.8179 (t70) cc_final: 0.7830 (t70) REVERT: A 101 TYR cc_start: 0.7206 (t80) cc_final: 0.6899 (t80) REVERT: A 169 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8281 (ttpp) REVERT: A 233 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7893 (mtm-85) REVERT: B 101 TYR cc_start: 0.7194 (t80) cc_final: 0.6797 (t80) REVERT: C 101 TYR cc_start: 0.7133 (t80) cc_final: 0.6850 (t80) outliers start: 29 outliers final: 22 residues processed: 206 average time/residue: 0.3985 time to fit residues: 88.2069 Evaluate side-chains 209 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 A residue 183 SER Chi-restraints excluded: chain A residue 233 ARG 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 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 231 LYS Chi-restraints excluded: chain D residue 35 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.197502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170936 restraints weight = 7242.382| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.55 r_work: 0.3829 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2279 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= 0.128 Angle : 0.575 6.407 10384 Z= 0.311 Chirality : 0.046 0.168 1208 Planarity : 0.004 0.033 1300 Dihedral : 6.354 39.696 1232 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.09 % Allowed : 25.62 % Favored : 71.29 % 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: 0.77 (0.28), residues: 336 loop : -0.90 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.017 0.001 TYR C 142 PHE 0.013 0.002 PHE B 68 TRP 0.004 0.001 TRP A 59 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7572) covalent geometry : angle 0.57136 (10360) hydrogen bonds : bond 0.03718 ( 322) hydrogen bonds : angle 4.81117 ( 1038) link_ALPHA1-6 : bond 0.00285 ( 4) link_ALPHA1-6 : angle 1.44675 ( 12) link_BETA1-2 : bond 0.00157 ( 4) link_BETA1-2 : angle 1.54002 ( 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 207 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.231 Fit side-chains REVERT: A 69 ASP cc_start: 0.8114 (t70) cc_final: 0.7799 (t70) REVERT: A 101 TYR cc_start: 0.7123 (t80) cc_final: 0.6818 (t80) REVERT: A 169 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8248 (ttpp) REVERT: B 69 ASP cc_start: 0.8061 (t70) cc_final: 0.7779 (t70) REVERT: B 101 TYR cc_start: 0.7148 (t80) cc_final: 0.6760 (t80) REVERT: C 101 TYR cc_start: 0.6934 (t80) cc_final: 0.6671 (t80) REVERT: D 101 TYR cc_start: 0.7055 (t80) cc_final: 0.6688 (t80) outliers start: 25 outliers final: 21 residues processed: 197 average time/residue: 0.4277 time to fit residues: 90.2031 Evaluate side-chains 202 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 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 A residue 183 SER 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 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 231 LYS Chi-restraints excluded: chain D residue 35 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 0.0670 chunk 41 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 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 = 0.4227 r_free = 0.4227 target = 0.195399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168674 restraints weight = 7203.303| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.53 r_work: 0.3812 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7580 Z= 0.168 Angle : 0.600 6.888 10384 Z= 0.325 Chirality : 0.046 0.165 1208 Planarity : 0.004 0.034 1300 Dihedral : 6.431 39.438 1232 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.71 % Allowed : 25.12 % 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: -0.33 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.82 (0.28), residues: 336 loop : -0.91 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.019 0.001 TYR B 142 PHE 0.015 0.002 PHE B 68 TRP 0.005 0.001 TRP A 59 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7572) covalent geometry : angle 0.59633 (10360) hydrogen bonds : bond 0.04093 ( 322) hydrogen bonds : angle 4.94514 ( 1038) link_ALPHA1-6 : bond 0.00295 ( 4) link_ALPHA1-6 : angle 1.37484 ( 12) link_BETA1-2 : bond 0.00205 ( 4) link_BETA1-2 : angle 1.53523 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.63 seconds wall clock time: 50 minutes 18.02 seconds (3018.02 seconds total)