Starting phenix.real_space_refine on Fri Sep 11 12:23:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.map" model { file = "/net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ye4_10789/09_2026/6ye4_10789.cif" } resolution = 3.2 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= 0.002 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 P 5 5.49 5 S 25 5.16 5 C 5780 2.51 5 N 1645 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "B" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "C" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "D" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "E" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 3.45, per 1000 atoms: 0.38 Number of scatterers: 9140 At special positions: 0 Unit cell: (82.7, 82.7, 130.666, 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) S 25 16.00 P 5 15.00 O 1685 8.00 N 1645 7.00 C 5780 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 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 649.3 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 90.9% alpha, 0.0% 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 48 through 55 removed outlier: 3.608A pdb=" N TYR A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 100 removed outlier: 4.515A pdb=" N SER A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 140 through 164 removed outlier: 3.800A pdb=" N GLY A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 199 Proline residue: A 178 - end of helix removed outlier: 3.643A pdb=" N SER A 199 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 280 removed outlier: 4.316A pdb=" N VAL A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Proline residue: A 209 - end of helix Proline residue: A 227 - end of helix removed outlier: 4.530A pdb=" N HIS A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.589A pdb=" N TYR B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 100 removed outlier: 4.520A pdb=" N SER B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 140 through 164 removed outlier: 3.779A pdb=" N GLY B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 199 Proline residue: B 178 - end of helix removed outlier: 3.640A pdb=" N SER B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 280 removed outlier: 4.328A pdb=" N VAL B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Proline residue: B 209 - end of helix Proline residue: B 227 - end of helix removed outlier: 4.412A pdb=" N HIS B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.583A pdb=" N TYR C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 100 removed outlier: 4.524A pdb=" N SER C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 140 through 164 removed outlier: 3.776A pdb=" N GLY C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 199 Proline residue: C 178 - end of helix removed outlier: 3.632A pdb=" N SER C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 280 removed outlier: 4.333A pdb=" N VAL C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Proline residue: C 209 - end of helix Proline residue: C 227 - end of helix removed outlier: 4.437A pdb=" N HIS C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 removed outlier: 3.602A pdb=" N TYR D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 100 removed outlier: 4.533A pdb=" N SER D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 140 through 164 removed outlier: 3.799A pdb=" N GLY D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 199 Proline residue: D 178 - end of helix removed outlier: 3.630A pdb=" N SER D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 280 removed outlier: 4.336A pdb=" N VAL D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Proline residue: D 209 - end of helix Proline residue: D 227 - end of helix removed outlier: 4.516A pdb=" N HIS D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.612A pdb=" N TYR E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 100 removed outlier: 4.519A pdb=" N SER E 83 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 120 through 135 Processing helix chain 'E' and resid 140 through 164 removed outlier: 3.779A pdb=" N GLY E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 199 Proline residue: E 178 - end of helix removed outlier: 3.626A pdb=" N SER E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 280 removed outlier: 4.326A pdb=" N VAL E 207 " --> pdb=" O ASN E 203 " (cutoff:3.500A) Proline residue: E 209 - end of helix Proline residue: E 227 - end of helix removed outlier: 4.418A pdb=" N HIS E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2524 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: 1.72 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1505 1.29 - 1.41: 2321 1.41 - 1.54: 5343 1.54 - 1.66: 46 1.66 - 1.79: 50 Bond restraints: 9265 Sorted by residual: bond pdb=" CB VAL B 229 " pdb=" CG2 VAL B 229 " ideal model delta sigma weight residual 1.521 1.387 0.134 3.30e-02 9.18e+02 1.64e+01 bond pdb=" CB VAL E 229 " pdb=" CG2 VAL E 229 " ideal model delta sigma weight residual 1.521 1.388 0.133 3.30e-02 9.18e+02 1.63e+01 bond pdb=" CB VAL C 229 " pdb=" CG2 VAL C 229 " ideal model delta sigma weight residual 1.521 1.388 0.133 3.30e-02 9.18e+02 1.63e+01 bond pdb=" CB VAL D 229 " pdb=" CG2 VAL D 229 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.60e+01 bond pdb=" CB VAL A 229 " pdb=" CG2 VAL A 229 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.59e+01 ... (remaining 9260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 12039 3.90 - 7.81: 391 7.81 - 11.71: 57 11.71 - 15.61: 13 15.61 - 19.52: 5 Bond angle restraints: 12505 Sorted by residual: angle pdb=" O3P PGT B 301 " pdb=" P PGT B 301 " pdb=" O4P PGT B 301 " ideal model delta sigma weight residual 92.82 112.34 -19.52 3.00e+00 1.11e-01 4.23e+01 angle pdb=" O3P PGT A 301 " pdb=" P PGT A 301 " pdb=" O4P PGT A 301 " ideal model delta sigma weight residual 92.82 111.94 -19.12 3.00e+00 1.11e-01 4.06e+01 angle pdb=" O3P PGT D 301 " pdb=" P PGT D 301 " pdb=" O4P PGT D 301 " ideal model delta sigma weight residual 92.82 111.92 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" CA GLU B 137 " pdb=" CB GLU B 137 " pdb=" CG GLU B 137 " ideal model delta sigma weight residual 114.10 125.39 -11.29 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CA GLU D 137 " pdb=" CB GLU D 137 " pdb=" CG GLU D 137 " ideal model delta sigma weight residual 114.10 125.35 -11.25 2.00e+00 2.50e-01 3.16e+01 ... (remaining 12500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.42: 4630 12.42 - 24.85: 607 24.85 - 37.27: 203 37.27 - 49.70: 75 49.70 - 62.12: 45 Dihedral angle restraints: 5560 sinusoidal: 2190 harmonic: 3370 Sorted by residual: dihedral pdb=" N GLU B 137 " pdb=" C GLU B 137 " pdb=" CA GLU B 137 " pdb=" CB GLU B 137 " ideal model delta harmonic sigma weight residual 122.80 130.98 -8.18 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N GLU C 137 " pdb=" C GLU C 137 " pdb=" CA GLU C 137 " pdb=" CB GLU C 137 " ideal model delta harmonic sigma weight residual 122.80 130.97 -8.17 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CG ARG B 271 " pdb=" CD ARG B 271 " pdb=" NE ARG B 271 " pdb=" CZ ARG B 271 " ideal model delta sinusoidal sigma weight residual 90.00 134.45 -44.45 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 713 0.065 - 0.130: 449 0.130 - 0.195: 202 0.195 - 0.260: 65 0.260 - 0.325: 21 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CG LEU B 216 " pdb=" CB LEU B 216 " pdb=" CD1 LEU B 216 " pdb=" CD2 LEU B 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU D 216 " pdb=" CB LEU D 216 " pdb=" CD1 LEU D 216 " pdb=" CD2 LEU D 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU E 216 " pdb=" CB LEU E 216 " pdb=" CD1 LEU E 216 " pdb=" CD2 LEU E 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1447 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 255 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C LEU E 255 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU E 255 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU E 256 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 255 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C LEU A 255 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU A 255 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 256 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 255 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C LEU D 255 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU D 255 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU D 256 " -0.024 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3333 2.88 - 3.38: 9023 3.38 - 3.89: 15032 3.89 - 4.39: 17315 4.39 - 4.90: 30078 Nonbonded interactions: 74781 Sorted by model distance: nonbonded pdb=" OD1 ASP A 248 " pdb=" NH1 ARG E 154 " model vdw 2.373 3.120 nonbonded pdb=" NH1 ARG B 154 " pdb=" OD1 ASP C 248 " model vdw 2.375 3.120 nonbonded pdb=" NH1 ARG D 154 " pdb=" OD1 ASP E 248 " model vdw 2.402 3.120 nonbonded pdb=" NH1 ARG C 154 " pdb=" OD1 ASP D 248 " model vdw 2.402 3.120 nonbonded pdb=" NH1 ARG A 154 " pdb=" OD1 ASP B 248 " model vdw 2.422 3.120 ... (remaining 74776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.110 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 : 0.026 0.144 9265 Z= 1.067 Angle : 1.692 19.517 12505 Z= 0.828 Chirality : 0.103 0.325 1450 Planarity : 0.010 0.058 1605 Dihedral : 14.611 62.122 3390 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.18), residues: 1175 helix: -1.79 (0.11), residues: 1060 sheet: None (None), residues: 0 loop : -4.08 (0.44), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 154 TYR 0.023 0.008 TYR C 53 PHE 0.041 0.008 PHE D 79 TRP 0.044 0.006 TRP C 50 HIS 0.023 0.004 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.02634 / 1.07 ( 9265) covalent geometry : angle 1.69231 / 0.83 (12505) hydrogen bonds : bond 0.11919 / 7.92 ( 843) hydrogen bonds : angle 5.82757 / 4.29 ( 2524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.317 Fit side-chains REVERT: A 52 MET cc_start: 0.8087 (mtp) cc_final: 0.7462 (mtt) REVERT: A 81 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8337 (tptt) REVERT: A 139 ASN cc_start: 0.7912 (m-40) cc_final: 0.7647 (p0) REVERT: B 81 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8376 (tttt) REVERT: C 81 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8355 (tttt) REVERT: C 126 ASN cc_start: 0.8013 (t0) cc_final: 0.7635 (m-40) REVERT: D 81 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8374 (tptt) REVERT: E 81 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8421 (tptt) REVERT: E 159 TYR cc_start: 0.8239 (t80) cc_final: 0.7969 (t80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0834 time to fit residues: 19.2014 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN B 130 ASN B 191 ASN C 130 ASN D 130 ASN D 191 ASN E 130 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111934 restraints weight = 32360.806| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.30 r_work: 0.2987 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9265 Z= 0.149 Angle : 0.519 6.434 12505 Z= 0.271 Chirality : 0.035 0.149 1450 Planarity : 0.005 0.035 1605 Dihedral : 8.904 59.754 1420 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.33 % Allowed : 11.78 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1175 helix: 0.95 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.82 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.009 0.002 TYR A 159 PHE 0.008 0.002 PHE E 179 TRP 0.008 0.001 TRP A 50 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 9265) covalent geometry : angle 0.51919 / 0.27 (12505) hydrogen bonds : bond 0.03576 / 2.39 ( 843) hydrogen bonds : angle 3.78843 / 2.79 ( 2524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.341 Fit side-chains REVERT: A 52 MET cc_start: 0.7376 (mtp) cc_final: 0.6699 (mtt) REVERT: A 81 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7704 (tptt) REVERT: A 96 GLN cc_start: 0.8736 (tt0) cc_final: 0.8482 (mt0) REVERT: A 133 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6484 (mt-10) REVERT: B 52 MET cc_start: 0.7554 (mtp) cc_final: 0.6762 (mtm) REVERT: B 81 LYS cc_start: 0.8353 (ttpp) cc_final: 0.7660 (tptt) REVERT: C 52 MET cc_start: 0.7392 (mtp) cc_final: 0.6577 (mtm) REVERT: C 81 LYS cc_start: 0.8466 (ttpp) cc_final: 0.7724 (tptt) REVERT: C 113 GLN cc_start: 0.8366 (tp40) cc_final: 0.8114 (tp40) REVERT: D 52 MET cc_start: 0.7482 (mtp) cc_final: 0.6799 (mtm) REVERT: D 81 LYS cc_start: 0.8433 (ttpp) cc_final: 0.7729 (tptt) REVERT: D 126 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7374 (t0) REVERT: D 204 LEU cc_start: 0.7623 (tt) cc_final: 0.7267 (tt) REVERT: E 52 MET cc_start: 0.7439 (mtp) cc_final: 0.6811 (mtp) REVERT: E 81 LYS cc_start: 0.8517 (ttpp) cc_final: 0.7712 (tptt) outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 0.0834 time to fit residues: 13.6738 Evaluate side-chains 95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN E 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113470 restraints weight = 27107.997| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.07 r_work: 0.3014 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9265 Z= 0.136 Angle : 0.486 5.942 12505 Z= 0.255 Chirality : 0.035 0.143 1450 Planarity : 0.004 0.032 1605 Dihedral : 8.092 59.888 1420 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.67 % Allowed : 14.33 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.24), residues: 1175 helix: 2.04 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.44 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.021 0.002 TYR A 159 PHE 0.006 0.001 PHE B 183 TRP 0.006 0.001 TRP C 50 HIS 0.002 0.000 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9265) covalent geometry : angle 0.48572 / 0.26 (12505) hydrogen bonds : bond 0.03364 / 2.25 ( 843) hydrogen bonds : angle 3.48898 / 2.56 ( 2524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.319 Fit side-chains REVERT: A 52 MET cc_start: 0.7423 (mtp) cc_final: 0.6740 (mtt) REVERT: A 81 LYS cc_start: 0.8478 (ttpp) cc_final: 0.7727 (tptt) REVERT: A 96 GLN cc_start: 0.8702 (tt0) cc_final: 0.8460 (mt0) REVERT: A 133 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6502 (mt-10) REVERT: B 52 MET cc_start: 0.7518 (mtp) cc_final: 0.6769 (mtm) REVERT: B 81 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7642 (tptt) REVERT: C 52 MET cc_start: 0.7336 (mtp) cc_final: 0.6558 (mtm) REVERT: C 81 LYS cc_start: 0.8460 (ttpp) cc_final: 0.7675 (tptt) REVERT: C 113 GLN cc_start: 0.8399 (tp40) cc_final: 0.8143 (tp40) REVERT: D 52 MET cc_start: 0.7535 (mtp) cc_final: 0.6853 (mtm) REVERT: D 81 LYS cc_start: 0.8433 (ttpp) cc_final: 0.7689 (tptt) REVERT: D 126 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7310 (t0) REVERT: D 159 TYR cc_start: 0.7865 (t80) cc_final: 0.7649 (t80) REVERT: E 52 MET cc_start: 0.7384 (mtp) cc_final: 0.6745 (mtp) REVERT: E 81 LYS cc_start: 0.8471 (ttpp) cc_final: 0.7656 (tptt) REVERT: E 159 TYR cc_start: 0.7825 (t80) cc_final: 0.7525 (t80) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 0.0816 time to fit residues: 11.8336 Evaluate side-chains 95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN E 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113243 restraints weight = 27877.075| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.06 r_work: 0.3010 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9265 Z= 0.136 Angle : 0.465 5.919 12505 Z= 0.242 Chirality : 0.035 0.130 1450 Planarity : 0.003 0.031 1605 Dihedral : 7.565 58.495 1420 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 14.67 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.25), residues: 1175 helix: 2.46 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.30 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.017 0.002 TYR B 159 PHE 0.006 0.001 PHE A 183 TRP 0.006 0.001 TRP B 50 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9265) covalent geometry : angle 0.46456 / 0.24 (12505) hydrogen bonds : bond 0.03322 / 2.22 ( 843) hydrogen bonds : angle 3.39222 / 2.49 ( 2524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.326 Fit side-chains REVERT: A 52 MET cc_start: 0.7417 (mtp) cc_final: 0.6715 (mtt) REVERT: A 81 LYS cc_start: 0.8458 (ttpp) cc_final: 0.7715 (tptt) REVERT: A 96 GLN cc_start: 0.8701 (tt0) cc_final: 0.8471 (mt0) REVERT: A 133 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6466 (mt-10) REVERT: A 159 TYR cc_start: 0.7887 (t80) cc_final: 0.7671 (t80) REVERT: B 52 MET cc_start: 0.7549 (mtp) cc_final: 0.6773 (mtm) REVERT: B 81 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7642 (tptt) REVERT: C 52 MET cc_start: 0.7298 (mtp) cc_final: 0.6560 (mtm) REVERT: C 81 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7696 (tptt) REVERT: C 96 GLN cc_start: 0.8755 (mt0) cc_final: 0.8535 (mt0) REVERT: C 113 GLN cc_start: 0.8355 (tp40) cc_final: 0.8123 (tp40) REVERT: C 252 GLN cc_start: 0.8308 (tt0) cc_final: 0.7765 (tt0) REVERT: D 52 MET cc_start: 0.7508 (mtp) cc_final: 0.6830 (mtm) REVERT: D 81 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7692 (tptt) REVERT: D 126 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7400 (t0) REVERT: E 52 MET cc_start: 0.7375 (mtp) cc_final: 0.6736 (mtp) REVERT: E 81 LYS cc_start: 0.8451 (ttpp) cc_final: 0.7635 (tptt) REVERT: E 160 SER cc_start: 0.8783 (p) cc_final: 0.8483 (m) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.0812 time to fit residues: 11.2029 Evaluate side-chains 95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114440 restraints weight = 22186.961| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.75 r_work: 0.3035 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9265 Z= 0.137 Angle : 0.459 5.886 12505 Z= 0.238 Chirality : 0.035 0.118 1450 Planarity : 0.003 0.031 1605 Dihedral : 7.274 59.916 1420 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.33 % Allowed : 14.56 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.25), residues: 1175 helix: 2.66 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.27 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.016 0.002 TYR D 159 PHE 0.006 0.001 PHE A 183 TRP 0.005 0.001 TRP B 50 HIS 0.002 0.000 HIS E 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9265) covalent geometry : angle 0.45898 / 0.24 (12505) hydrogen bonds : bond 0.03312 / 2.21 ( 843) hydrogen bonds : angle 3.36861 / 2.48 ( 2524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.316 Fit side-chains REVERT: A 52 MET cc_start: 0.7521 (mtp) cc_final: 0.6796 (mtt) REVERT: A 81 LYS cc_start: 0.8524 (ttpp) cc_final: 0.7817 (tptt) REVERT: A 96 GLN cc_start: 0.8711 (tt0) cc_final: 0.8495 (mt0) REVERT: B 52 MET cc_start: 0.7614 (mtp) cc_final: 0.6842 (mtm) REVERT: B 81 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7706 (tptt) REVERT: B 159 TYR cc_start: 0.7967 (t80) cc_final: 0.7701 (t80) REVERT: C 52 MET cc_start: 0.7457 (mtp) cc_final: 0.6727 (mtm) REVERT: C 81 LYS cc_start: 0.8482 (ttpp) cc_final: 0.7757 (tptt) REVERT: C 96 GLN cc_start: 0.8783 (mt0) cc_final: 0.8573 (mt0) REVERT: C 113 GLN cc_start: 0.8317 (tp40) cc_final: 0.8096 (tp40) REVERT: C 252 GLN cc_start: 0.8323 (tt0) cc_final: 0.7782 (tt0) REVERT: D 52 MET cc_start: 0.7552 (mtp) cc_final: 0.6880 (mtm) REVERT: D 81 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7824 (tptt) REVERT: D 126 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7453 (t0) REVERT: E 52 MET cc_start: 0.7440 (mtp) cc_final: 0.6799 (mtp) REVERT: E 81 LYS cc_start: 0.8493 (ttpp) cc_final: 0.7714 (tptt) REVERT: E 160 SER cc_start: 0.8804 (p) cc_final: 0.8487 (m) outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.0805 time to fit residues: 11.6027 Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112291 restraints weight = 29590.908| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.22 r_work: 0.2993 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9265 Z= 0.139 Angle : 0.455 5.885 12505 Z= 0.237 Chirality : 0.035 0.115 1450 Planarity : 0.003 0.031 1605 Dihedral : 7.151 59.365 1420 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.11 % Allowed : 14.44 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.24), residues: 1175 helix: 2.77 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.22 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.017 0.002 TYR A 159 PHE 0.006 0.001 PHE B 183 TRP 0.005 0.001 TRP B 50 HIS 0.002 0.000 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9265) covalent geometry : angle 0.45513 / 0.24 (12505) hydrogen bonds : bond 0.03322 / 2.22 ( 843) hydrogen bonds : angle 3.36269 / 2.47 ( 2524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.332 Fit side-chains REVERT: A 52 MET cc_start: 0.7447 (mtp) cc_final: 0.6726 (mtt) REVERT: A 81 LYS cc_start: 0.8506 (ttpp) cc_final: 0.7784 (tptt) REVERT: A 96 GLN cc_start: 0.8701 (tt0) cc_final: 0.8486 (mt0) REVERT: B 52 MET cc_start: 0.7573 (mtp) cc_final: 0.6780 (mtm) REVERT: B 81 LYS cc_start: 0.8356 (ttpp) cc_final: 0.7661 (tptt) REVERT: B 159 TYR cc_start: 0.7974 (t80) cc_final: 0.7706 (t80) REVERT: C 52 MET cc_start: 0.7396 (mtp) cc_final: 0.6658 (mtm) REVERT: C 81 LYS cc_start: 0.8451 (ttpp) cc_final: 0.7719 (tptt) REVERT: C 113 GLN cc_start: 0.8298 (tp40) cc_final: 0.8087 (tp40) REVERT: C 252 GLN cc_start: 0.8312 (tt0) cc_final: 0.7766 (tt0) REVERT: D 52 MET cc_start: 0.7536 (mtp) cc_final: 0.6846 (mtm) REVERT: D 81 LYS cc_start: 0.8425 (ttpp) cc_final: 0.7788 (tptt) REVERT: D 113 GLN cc_start: 0.8332 (tp40) cc_final: 0.8102 (mm-40) REVERT: D 126 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7434 (t0) REVERT: E 52 MET cc_start: 0.7362 (mtp) cc_final: 0.6713 (mtp) REVERT: E 81 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7681 (tptt) outliers start: 10 outliers final: 9 residues processed: 92 average time/residue: 0.0833 time to fit residues: 11.4358 Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114105 restraints weight = 30410.845| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.28 r_work: 0.3018 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9265 Z= 0.117 Angle : 0.432 5.788 12505 Z= 0.226 Chirality : 0.034 0.112 1450 Planarity : 0.003 0.031 1605 Dihedral : 6.800 57.864 1420 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.22 % Allowed : 14.89 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.77 (0.25), residues: 1175 helix: 2.98 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.12 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 259 TYR 0.014 0.002 TYR C 159 PHE 0.005 0.001 PHE E 169 TRP 0.004 0.001 TRP E 75 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9265) covalent geometry : angle 0.43186 / 0.23 (12505) hydrogen bonds : bond 0.03162 / 2.11 ( 843) hydrogen bonds : angle 3.23556 / 2.38 ( 2524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.272 Fit side-chains REVERT: A 52 MET cc_start: 0.7345 (mtp) cc_final: 0.6551 (mtm) REVERT: A 81 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7796 (tptt) REVERT: B 52 MET cc_start: 0.7466 (mtp) cc_final: 0.6757 (mtm) REVERT: B 81 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7576 (tptt) REVERT: B 159 TYR cc_start: 0.7922 (t80) cc_final: 0.7668 (t80) REVERT: C 52 MET cc_start: 0.7277 (mtp) cc_final: 0.6516 (mtm) REVERT: C 81 LYS cc_start: 0.8449 (ttpp) cc_final: 0.7739 (tptt) REVERT: C 113 GLN cc_start: 0.8282 (tp40) cc_final: 0.8069 (tp40) REVERT: C 252 GLN cc_start: 0.8309 (tt0) cc_final: 0.7774 (tt0) REVERT: D 52 MET cc_start: 0.7432 (mtp) cc_final: 0.6786 (mtm) REVERT: D 81 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7768 (tptt) REVERT: D 113 GLN cc_start: 0.8341 (tp40) cc_final: 0.8124 (mm-40) REVERT: D 126 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7307 (t0) REVERT: D 252 GLN cc_start: 0.8298 (tt0) cc_final: 0.7826 (tt0) REVERT: E 52 MET cc_start: 0.7333 (mtp) cc_final: 0.6659 (mtp) REVERT: E 81 LYS cc_start: 0.8384 (ttpp) cc_final: 0.7722 (tptt) outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.0789 time to fit residues: 11.7213 Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 0.0570 chunk 106 optimal weight: 0.7980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.153195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116568 restraints weight = 25180.515| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.91 r_work: 0.3071 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9265 Z= 0.105 Angle : 0.419 5.722 12505 Z= 0.219 Chirality : 0.033 0.111 1450 Planarity : 0.003 0.031 1605 Dihedral : 6.547 56.791 1420 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.11 % Allowed : 15.33 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.25), residues: 1175 helix: 3.17 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.06 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 259 TYR 0.026 0.002 TYR E 159 PHE 0.005 0.001 PHE D 169 TRP 0.004 0.000 TRP B 75 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 9265) covalent geometry : angle 0.41868 / 0.22 (12505) hydrogen bonds : bond 0.03046 / 2.03 ( 843) hydrogen bonds : angle 3.12343 / 2.29 ( 2524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.353 Fit side-chains REVERT: A 52 MET cc_start: 0.7372 (mtp) cc_final: 0.6610 (mtm) REVERT: A 81 LYS cc_start: 0.8475 (ttpp) cc_final: 0.7846 (tptt) REVERT: B 52 MET cc_start: 0.7499 (mtp) cc_final: 0.6833 (mtm) REVERT: B 81 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7626 (tptt) REVERT: B 159 TYR cc_start: 0.7916 (t80) cc_final: 0.7685 (t80) REVERT: B 204 LEU cc_start: 0.7677 (tt) cc_final: 0.7339 (tt) REVERT: C 52 MET cc_start: 0.7357 (mtp) cc_final: 0.6613 (mtm) REVERT: C 81 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7768 (tptt) REVERT: C 113 GLN cc_start: 0.8230 (tp40) cc_final: 0.8023 (tp40) REVERT: C 252 GLN cc_start: 0.8309 (tt0) cc_final: 0.7786 (tt0) REVERT: D 52 MET cc_start: 0.7429 (mtp) cc_final: 0.6810 (mtm) REVERT: D 81 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7812 (tptt) REVERT: D 113 GLN cc_start: 0.8324 (tp40) cc_final: 0.8101 (mm-40) REVERT: D 252 GLN cc_start: 0.8313 (tt0) cc_final: 0.7845 (tt0) REVERT: E 52 MET cc_start: 0.7329 (mtp) cc_final: 0.6614 (mtm) REVERT: E 81 LYS cc_start: 0.8471 (ttpp) cc_final: 0.7825 (tptt) outliers start: 10 outliers final: 9 residues processed: 106 average time/residue: 0.0798 time to fit residues: 12.7738 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112822 restraints weight = 32032.927| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.37 r_work: 0.3002 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9265 Z= 0.131 Angle : 0.444 5.835 12505 Z= 0.230 Chirality : 0.035 0.112 1450 Planarity : 0.003 0.031 1605 Dihedral : 6.809 57.260 1420 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.22 % Allowed : 16.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.24), residues: 1175 helix: 3.10 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.05 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.021 0.002 TYR A 159 PHE 0.006 0.001 PHE A 169 TRP 0.005 0.001 TRP C 50 HIS 0.002 0.000 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9265) covalent geometry : angle 0.44444 / 0.23 (12505) hydrogen bonds : bond 0.03221 / 2.15 ( 843) hydrogen bonds : angle 3.25625 / 2.39 ( 2524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.322 Fit side-chains REVERT: A 52 MET cc_start: 0.7399 (mtp) cc_final: 0.6648 (mtt) REVERT: A 81 LYS cc_start: 0.8499 (ttpp) cc_final: 0.7787 (tptt) REVERT: B 52 MET cc_start: 0.7562 (mtp) cc_final: 0.6820 (mtm) REVERT: B 81 LYS cc_start: 0.8367 (ttpp) cc_final: 0.7676 (tptt) REVERT: B 159 TYR cc_start: 0.7971 (t80) cc_final: 0.7708 (t80) REVERT: B 204 LEU cc_start: 0.7609 (tt) cc_final: 0.7261 (tt) REVERT: C 52 MET cc_start: 0.7308 (mtp) cc_final: 0.6593 (mtm) REVERT: C 81 LYS cc_start: 0.8442 (ttpp) cc_final: 0.7718 (tptt) REVERT: C 113 GLN cc_start: 0.8205 (tp40) cc_final: 0.8001 (tp40) REVERT: C 252 GLN cc_start: 0.8331 (tt0) cc_final: 0.7794 (tt0) REVERT: D 52 MET cc_start: 0.7491 (mtp) cc_final: 0.6813 (mtm) REVERT: D 81 LYS cc_start: 0.8410 (ttpp) cc_final: 0.7783 (tptt) REVERT: D 113 GLN cc_start: 0.8338 (tp40) cc_final: 0.8121 (mm-40) REVERT: E 52 MET cc_start: 0.7367 (mtp) cc_final: 0.6672 (mtp) REVERT: E 81 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7690 (tptt) outliers start: 11 outliers final: 11 residues processed: 96 average time/residue: 0.0789 time to fit residues: 11.3332 Evaluate side-chains 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.0030 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114112 restraints weight = 27384.873| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.10 r_work: 0.3023 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9265 Z= 0.121 Angle : 0.433 5.795 12505 Z= 0.226 Chirality : 0.034 0.110 1450 Planarity : 0.003 0.031 1605 Dihedral : 6.751 59.520 1420 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.33 % Allowed : 16.00 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.24), residues: 1175 helix: 3.16 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.98 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.027 0.002 TYR E 159 PHE 0.006 0.001 PHE A 169 TRP 0.004 0.001 TRP D 50 HIS 0.001 0.000 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9265) covalent geometry : angle 0.43314 / 0.23 (12505) hydrogen bonds : bond 0.03169 / 2.12 ( 843) hydrogen bonds : angle 3.22784 / 2.37 ( 2524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.337 Fit side-chains REVERT: A 52 MET cc_start: 0.7435 (mtp) cc_final: 0.6637 (mtm) REVERT: A 81 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7807 (tptt) REVERT: B 52 MET cc_start: 0.7553 (mtp) cc_final: 0.6832 (mtm) REVERT: B 81 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7712 (tptt) REVERT: B 159 TYR cc_start: 0.7973 (t80) cc_final: 0.7720 (t80) REVERT: B 204 LEU cc_start: 0.7631 (tt) cc_final: 0.7324 (tt) REVERT: C 52 MET cc_start: 0.7358 (mtp) cc_final: 0.6634 (mtm) REVERT: C 81 LYS cc_start: 0.8487 (ttpp) cc_final: 0.7768 (tptt) REVERT: C 113 GLN cc_start: 0.8219 (tp40) cc_final: 0.8017 (tp40) REVERT: C 252 GLN cc_start: 0.8339 (tt0) cc_final: 0.7802 (tt0) REVERT: D 52 MET cc_start: 0.7492 (mtp) cc_final: 0.6829 (mtm) REVERT: D 81 LYS cc_start: 0.8433 (ttpp) cc_final: 0.7823 (tptt) REVERT: D 126 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7278 (t0) REVERT: E 52 MET cc_start: 0.7390 (mtp) cc_final: 0.6709 (mtp) REVERT: E 81 LYS cc_start: 0.8452 (ttpp) cc_final: 0.7750 (tptt) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.0728 time to fit residues: 10.6417 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 13 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.153060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115590 restraints weight = 28604.931| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.19 r_work: 0.3046 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9265 Z= 0.104 Angle : 0.429 8.987 12505 Z= 0.222 Chirality : 0.033 0.109 1450 Planarity : 0.003 0.030 1605 Dihedral : 6.543 56.505 1420 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 16.22 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.24), residues: 1175 helix: 3.29 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.95 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 165 TYR 0.028 0.002 TYR E 159 PHE 0.005 0.001 PHE E 169 TRP 0.004 0.001 TRP B 75 HIS 0.002 0.000 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 9265) covalent geometry : angle 0.42905 / 0.22 (12505) hydrogen bonds : bond 0.03058 / 2.05 ( 843) hydrogen bonds : angle 3.13532 / 2.30 ( 2524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.31 seconds wall clock time: 34 minutes 52.30 seconds (2092.30 seconds total)