Starting phenix.real_space_refine on Sat Aug 23 03:05:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ye4_10789/08_2025/6ye4_10789.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ye4_10789/08_2025/6ye4_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ye4_10789/08_2025/6ye4_10789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ye4_10789/08_2025/6ye4_10789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ye4_10789/08_2025/6ye4_10789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ye4_10789/08_2025/6ye4_10789.map" } 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-2.0-5787/lib/python3.9/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: 4.20, per 1000 atoms: 0.46 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: 1.00 Conformation dependent library (CDL) restraints added in 709.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 1.45 Time building geometry restraints manager: 1.25 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 - 15.81: 4844 15.81 - 31.63: 586 31.63 - 47.44: 141 47.44 - 63.26: 59 63.26 - 79.07: 5 Dihedral angle restraints: 5635 sinusoidal: 2265 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 5632 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: 3.900 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.000 Find NCS groups from input model: 0.100 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 15.502 79.073 3465 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 aren 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 covalent geometry : bond 0.02634 ( 9265) covalent geometry : angle 1.69231 (12505) hydrogen bonds : bond 0.11919 ( 843) hydrogen bonds : angle 5.82757 ( 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 : 0.347 Fit side-chains REVERT: A 52 MET cc_start: 0.8087 (mtp) cc_final: 0.7463 (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: 0.8747 (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: 0.8420 (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: 0.0866 time to fit residues: 19.6611 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 : 0.383 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3667 r_free = 0.3667 target = 0.150473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.112226 restraints weight = 32178.680| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.29 r_work: 0.2990 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9265 Z= 0.151 Angle : 0.521 6.594 12505 Z= 0.271 Chirality : 0.035 0.148 1450 Planarity : 0.005 0.035 1605 Dihedral : 11.627 74.575 1495 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.22 % Allowed : 11.89 % 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 aren not related in a simple way. whole: 0.74 (0.23), residues: 1175 helix: 0.97 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.81 (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 D 159 PHE 0.008 0.002 PHE E 179 TRP 0.007 0.001 TRP A 50 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9265) covalent geometry : angle 0.52126 (12505) hydrogen bonds : bond 0.03549 ( 843) hydrogen bonds : angle 3.76145 ( 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 113 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.391 Fit side-chains REVERT: A 52 MET cc_start: 0.7386 (mtp) cc_final: 0.6707 (mtt) REVERT: A 81 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7716 (tptt) REVERT: A 96 GLN cc_start: 0.8724 (tt0) cc_final: 0.8476 (mt0) REVERT: A 133 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6466 (mt-10) REVERT: B 52 MET cc_start: 0.7555 (mtp) cc_final: 0.6771 (mtm) REVERT: B 81 LYS cc_start: 0.8359 (ttpp) cc_final: 0.7668 (tptt) REVERT: C 52 MET cc_start: 0.7394 (mtp) cc_final: 0.6579 (mtm) REVERT: C 81 LYS cc_start: 0.8470 (ttpp) cc_final: 0.7736 (tptt) REVERT: C 113 GLN cc_start: 0.8371 (tp40) cc_final: 0.8121 (tp40) REVERT: D 52 MET cc_start: 0.7502 (mtp) cc_final: 0.6806 (mtm) REVERT: D 81 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7731 (tptt) REVERT: D 204 LEU cc_start: 0.7631 (tt) cc_final: 0.7273 (tt) REVERT: E 52 MET cc_start: 0.7437 (mtp) cc_final: 0.6826 (mtp) REVERT: E 81 LYS cc_start: 0.8551 (ttpp) cc_final: 0.7720 (tptt) outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.0929 time to fit residues: 15.1888 Evaluate side-chains 95 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3670 r_free = 0.3670 target = 0.151073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113498 restraints weight = 26643.262| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.05 r_work: 0.3019 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2146 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= 0.135 Angle : 0.488 5.942 12505 Z= 0.256 Chirality : 0.035 0.139 1450 Planarity : 0.004 0.031 1605 Dihedral : 9.843 56.610 1495 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.00 % Allowed : 13.89 % Favored : 85.11 % 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 aren not related in a simple way. whole: 2.41 (0.24), residues: 1175 helix: 2.08 (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 0.005 0.001 TRP C 50 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9265) covalent geometry : angle 0.48787 (12505) hydrogen bonds : bond 0.03349 ( 843) hydrogen bonds : angle 3.47291 ( 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 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.423 Fit side-chains REVERT: A 52 MET cc_start: 0.7397 (mtp) cc_final: 0.6719 (mtt) REVERT: A 81 LYS cc_start: 0.8454 (ttpp) cc_final: 0.7704 (tptt) REVERT: A 96 GLN cc_start: 0.8673 (tt0) cc_final: 0.8431 (mt0) REVERT: A 133 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6448 (mt-10) REVERT: B 52 MET cc_start: 0.7488 (mtp) cc_final: 0.6755 (mtm) REVERT: B 81 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7626 (tptt) REVERT: B 162 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8258 (t160) REVERT: C 52 MET cc_start: 0.7319 (mtp) cc_final: 0.6574 (mtm) REVERT: C 81 LYS cc_start: 0.8434 (ttpp) cc_final: 0.7648 (tptt) REVERT: C 113 GLN cc_start: 0.8387 (tp40) cc_final: 0.8127 (tp40) REVERT: C 220 MET cc_start: 0.8576 (ttm) cc_final: 0.8368 (ttm) REVERT: D 52 MET cc_start: 0.7520 (mtp) cc_final: 0.6848 (mtm) REVERT: D 81 LYS cc_start: 0.8410 (ttpp) cc_final: 0.7663 (tptt) REVERT: D 126 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7294 (t0) REVERT: D 159 TYR cc_start: 0.7840 (t80) cc_final: 0.7622 (t80) REVERT: E 52 MET cc_start: 0.7353 (mtp) cc_final: 0.6726 (mtp) REVERT: E 81 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7637 (tptt) REVERT: E 159 TYR cc_start: 0.7802 (t80) cc_final: 0.7495 (t80) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 0.0902 time to fit residues: 13.1738 Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 162 ASN 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 E 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: 0.7980 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.0170 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115063 restraints weight = 27884.447| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.11 r_work: 0.3039 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 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 = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2432 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= 0.112 Angle : 0.444 5.794 12505 Z= 0.231 Chirality : 0.033 0.124 1450 Planarity : 0.003 0.029 1605 Dihedral : 8.795 50.910 1495 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.22 % Allowed : 15.33 % 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 aren not related in a simple way. whole: 3.27 (0.25), residues: 1175 helix: 2.64 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -3.21 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.018 0.002 TYR C 159 PHE 0.005 0.001 PHE D 169 TRP 0.003 0.001 TRP B 75 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9265) covalent geometry : angle 0.44379 (12505) hydrogen bonds : bond 0.03132 ( 843) hydrogen bonds : angle 3.24523 ( 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 102 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.382 Fit side-chains REVERT: A 52 MET cc_start: 0.7393 (mtp) cc_final: 0.6616 (mtm) REVERT: A 81 LYS cc_start: 0.8452 (ttpp) cc_final: 0.7800 (tptt) REVERT: A 96 GLN cc_start: 0.8656 (tt0) cc_final: 0.8452 (mt0) REVERT: B 52 MET cc_start: 0.7492 (mtp) cc_final: 0.6777 (mtm) REVERT: B 81 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7659 (tptt) REVERT: C 52 MET cc_start: 0.7199 (mtp) cc_final: 0.6472 (mtm) REVERT: C 81 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7721 (tptt) REVERT: C 96 GLN cc_start: 0.8717 (mt0) cc_final: 0.8503 (mt0) REVERT: C 113 GLN cc_start: 0.8329 (tp40) cc_final: 0.8092 (tp40) REVERT: C 252 GLN cc_start: 0.8301 (tt0) cc_final: 0.7772 (tt0) REVERT: D 52 MET cc_start: 0.7446 (mtp) cc_final: 0.6812 (mtm) REVERT: D 81 LYS cc_start: 0.8386 (ttpp) cc_final: 0.7772 (tptt) REVERT: D 126 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7341 (t0) REVERT: E 52 MET cc_start: 0.7328 (mtp) cc_final: 0.6621 (mtm) REVERT: E 81 LYS cc_start: 0.8417 (ttpp) cc_final: 0.7643 (tptt) REVERT: E 160 SER cc_start: 0.8756 (p) cc_final: 0.8478 (m) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.0829 time to fit residues: 12.4710 Evaluate side-chains 93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 220 MET 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: 0.8980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN E 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113659 restraints weight = 22051.542| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.74 r_work: 0.3026 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 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 = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9265 Z= 0.156 Angle : 0.480 5.935 12505 Z= 0.247 Chirality : 0.036 0.119 1450 Planarity : 0.003 0.030 1605 Dihedral : 9.000 52.461 1495 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 15.22 % 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 aren not related in a simple way. whole: 3.25 (0.25), residues: 1175 helix: 2.63 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.28 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.021 0.002 TYR C 159 PHE 0.007 0.001 PHE B 183 TRP 0.007 0.001 TRP B 50 HIS 0.003 0.000 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9265) covalent geometry : angle 0.47953 (12505) hydrogen bonds : bond 0.03404 ( 843) hydrogen bonds : angle 3.42155 ( 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 101 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.350 Fit side-chains REVERT: A 52 MET cc_start: 0.7459 (mtp) cc_final: 0.6745 (mtt) REVERT: A 81 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7737 (tptt) REVERT: A 96 GLN cc_start: 0.8705 (tt0) cc_final: 0.8467 (mt0) REVERT: B 52 MET cc_start: 0.7585 (mtp) cc_final: 0.6796 (mtm) REVERT: B 81 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7683 (tptt) REVERT: C 52 MET cc_start: 0.7415 (mtp) cc_final: 0.6661 (mtm) REVERT: C 81 LYS cc_start: 0.8468 (ttpp) cc_final: 0.7733 (tptt) REVERT: C 113 GLN cc_start: 0.8291 (tp40) cc_final: 0.8059 (tp40) REVERT: C 252 GLN cc_start: 0.8276 (tt0) cc_final: 0.7730 (tt0) REVERT: D 52 MET cc_start: 0.7549 (mtp) cc_final: 0.6868 (mtm) REVERT: D 81 LYS cc_start: 0.8421 (ttpp) cc_final: 0.7712 (tptt) REVERT: D 126 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7418 (t0) REVERT: E 52 MET cc_start: 0.7417 (mtp) cc_final: 0.6763 (mtp) REVERT: E 81 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7685 (tptt) REVERT: E 160 SER cc_start: 0.8720 (p) cc_final: 0.8518 (m) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.0888 time to fit residues: 12.3345 Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111957 restraints weight = 29578.315| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.19 r_work: 0.2988 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9265 Z= 0.152 Angle : 0.470 5.940 12505 Z= 0.243 Chirality : 0.035 0.115 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.983 55.833 1495 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.89 % Allowed : 15.33 % Favored : 83.78 % 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 aren not related in a simple way. whole: 3.35 (0.24), residues: 1175 helix: 2.70 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.28 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.016 0.002 TYR C 159 PHE 0.007 0.001 PHE B 183 TRP 0.006 0.001 TRP B 50 HIS 0.002 0.000 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9265) covalent geometry : angle 0.47026 (12505) hydrogen bonds : bond 0.03397 ( 843) hydrogen bonds : angle 3.41790 ( 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 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.369 Fit side-chains REVERT: A 52 MET cc_start: 0.7408 (mtp) cc_final: 0.6695 (mtt) REVERT: A 81 LYS cc_start: 0.8493 (ttpp) cc_final: 0.7758 (tptt) REVERT: A 96 GLN cc_start: 0.8685 (tt0) cc_final: 0.8442 (mt0) REVERT: B 52 MET cc_start: 0.7508 (mtp) cc_final: 0.6735 (mtm) REVERT: B 81 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7652 (tptt) REVERT: B 159 TYR cc_start: 0.7836 (t80) cc_final: 0.7503 (t80) REVERT: C 52 MET cc_start: 0.7393 (mtp) cc_final: 0.6639 (mtm) REVERT: C 81 LYS cc_start: 0.8448 (ttpp) cc_final: 0.7712 (tptt) REVERT: C 113 GLN cc_start: 0.8298 (tp40) cc_final: 0.8080 (tp40) REVERT: C 252 GLN cc_start: 0.8302 (tt0) cc_final: 0.7757 (tt0) REVERT: D 52 MET cc_start: 0.7503 (mtp) cc_final: 0.6845 (mtm) REVERT: D 81 LYS cc_start: 0.8402 (ttpp) cc_final: 0.7757 (tptt) REVERT: D 113 GLN cc_start: 0.8302 (tp40) cc_final: 0.8070 (mm-40) REVERT: D 126 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7418 (t0) REVERT: E 52 MET cc_start: 0.7390 (mtp) cc_final: 0.6736 (mtp) REVERT: E 81 LYS cc_start: 0.8447 (ttpp) cc_final: 0.7676 (tptt) outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 0.0896 time to fit residues: 12.3269 Evaluate side-chains 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113589 restraints weight = 30438.489| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.30 r_work: 0.3008 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2454 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= 0.120 Angle : 0.437 5.810 12505 Z= 0.227 Chirality : 0.034 0.113 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.645 58.817 1495 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 15.89 % Favored : 83.22 % 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 aren not related in a simple way. whole: 3.76 (0.24), residues: 1175 helix: 2.97 (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 0.002 0.000 ARG D 259 TYR 0.016 0.002 TYR C 159 PHE 0.005 0.001 PHE A 169 TRP 0.004 0.001 TRP E 75 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9265) covalent geometry : angle 0.43679 (12505) hydrogen bonds : bond 0.03185 ( 843) hydrogen bonds : angle 3.25977 ( 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 101 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.346 Fit side-chains REVERT: A 52 MET cc_start: 0.7428 (mtp) cc_final: 0.6636 (mtm) REVERT: A 81 LYS cc_start: 0.8513 (ttpp) cc_final: 0.7895 (tptt) REVERT: A 96 GLN cc_start: 0.8707 (tt0) cc_final: 0.8500 (mt0) REVERT: B 52 MET cc_start: 0.7525 (mtp) cc_final: 0.6798 (mtm) REVERT: B 81 LYS cc_start: 0.8395 (ttpp) cc_final: 0.7664 (tptt) REVERT: B 159 TYR cc_start: 0.7840 (t80) cc_final: 0.7552 (t80) REVERT: C 52 MET cc_start: 0.7334 (mtp) cc_final: 0.6603 (mtm) REVERT: C 81 LYS cc_start: 0.8507 (ttpp) cc_final: 0.7815 (tptt) REVERT: C 113 GLN cc_start: 0.8333 (tp40) cc_final: 0.8115 (tp40) REVERT: C 252 GLN cc_start: 0.8366 (tt0) cc_final: 0.7847 (tt0) REVERT: D 52 MET cc_start: 0.7505 (mtp) cc_final: 0.6843 (mtm) REVERT: D 81 LYS cc_start: 0.8428 (ttpp) cc_final: 0.7828 (tptt) REVERT: D 113 GLN cc_start: 0.8362 (tp40) cc_final: 0.8139 (mm-40) REVERT: E 52 MET cc_start: 0.7409 (mtp) cc_final: 0.6654 (mtm) REVERT: E 81 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7797 (tptt) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.0904 time to fit residues: 12.4191 Evaluate side-chains 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 192 SER 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: 0.6980 chunk 103 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114814 restraints weight = 25233.282| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.96 r_work: 0.3038 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2511 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= 0.122 Angle : 0.442 5.804 12505 Z= 0.230 Chirality : 0.034 0.143 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.636 59.028 1495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.00 % Allowed : 15.89 % Favored : 83.11 % 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 aren not related in a simple way. whole: 3.89 (0.24), residues: 1175 helix: 3.05 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.08 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.020 0.002 TYR A 159 PHE 0.005 0.001 PHE A 169 TRP 0.004 0.001 TRP B 50 HIS 0.002 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9265) covalent geometry : angle 0.44229 (12505) hydrogen bonds : bond 0.03185 ( 843) hydrogen bonds : angle 3.25174 ( 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 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.359 Fit side-chains REVERT: A 52 MET cc_start: 0.7410 (mtp) cc_final: 0.6617 (mtm) REVERT: A 81 LYS cc_start: 0.8468 (ttpp) cc_final: 0.7776 (tptt) REVERT: A 96 GLN cc_start: 0.8668 (tt0) cc_final: 0.8464 (mt0) REVERT: B 52 MET cc_start: 0.7496 (mtp) cc_final: 0.6776 (mtm) REVERT: B 81 LYS cc_start: 0.8354 (ttpp) cc_final: 0.7617 (tptt) REVERT: B 159 TYR cc_start: 0.7762 (t80) cc_final: 0.7475 (t80) REVERT: C 52 MET cc_start: 0.7299 (mtp) cc_final: 0.6575 (mtm) REVERT: C 81 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7731 (tptt) REVERT: C 113 GLN cc_start: 0.8240 (tp40) cc_final: 0.8023 (tp40) REVERT: C 252 GLN cc_start: 0.8305 (tt0) cc_final: 0.7784 (tt0) REVERT: D 52 MET cc_start: 0.7465 (mtp) cc_final: 0.6800 (mtm) REVERT: D 81 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7774 (tptt) REVERT: D 113 GLN cc_start: 0.8336 (tp40) cc_final: 0.8099 (mm-40) REVERT: E 52 MET cc_start: 0.7345 (mtp) cc_final: 0.6654 (mtp) REVERT: E 81 LYS cc_start: 0.8403 (ttpp) cc_final: 0.7672 (tptt) outliers start: 9 outliers final: 8 residues processed: 96 average time/residue: 0.0857 time to fit residues: 12.2439 Evaluate side-chains 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112624 restraints weight = 31949.192| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.37 r_work: 0.2992 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2463 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= 0.134 Angle : 0.448 5.847 12505 Z= 0.233 Chirality : 0.035 0.112 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.725 59.885 1495 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 16.11 % Favored : 83.00 % 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 aren not related in a simple way. whole: 3.88 (0.24), residues: 1175 helix: 3.04 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.04 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 259 TYR 0.033 0.002 TYR E 159 PHE 0.006 0.001 PHE A 169 TRP 0.004 0.001 TRP B 50 HIS 0.002 0.000 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9265) covalent geometry : angle 0.44789 (12505) hydrogen bonds : bond 0.03252 ( 843) hydrogen bonds : angle 3.29990 ( 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 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.380 Fit side-chains REVERT: A 52 MET cc_start: 0.7416 (mtp) cc_final: 0.6593 (mtm) REVERT: A 81 LYS cc_start: 0.8510 (ttpp) cc_final: 0.7801 (tptt) REVERT: A 96 GLN cc_start: 0.8662 (tt0) cc_final: 0.8443 (mt0) REVERT: B 52 MET cc_start: 0.7542 (mtp) cc_final: 0.6776 (mtm) REVERT: B 81 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7682 (tptt) REVERT: B 204 LEU cc_start: 0.7641 (tt) cc_final: 0.7301 (tt) REVERT: C 52 MET cc_start: 0.7334 (mtp) cc_final: 0.6603 (mtm) REVERT: C 81 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7762 (tptt) REVERT: C 113 GLN cc_start: 0.8262 (tp40) cc_final: 0.8045 (tp40) REVERT: C 252 GLN cc_start: 0.8337 (tt0) cc_final: 0.7805 (tt0) REVERT: D 52 MET cc_start: 0.7491 (mtp) cc_final: 0.6808 (mtm) REVERT: D 81 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7785 (tptt) REVERT: D 113 GLN cc_start: 0.8337 (tp40) cc_final: 0.8103 (mm-40) REVERT: E 52 MET cc_start: 0.7371 (mtp) cc_final: 0.6667 (mtp) REVERT: E 81 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7686 (tptt) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.0867 time to fit residues: 11.5589 Evaluate side-chains 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 153 GLU Chi-restraints excluded: chain D residue 192 SER 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: 0.0050 chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 0.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.155507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118964 restraints weight = 27537.665| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.05 r_work: 0.3102 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2757 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= 0.099 Angle : 0.418 5.667 12505 Z= 0.220 Chirality : 0.033 0.118 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.349 58.798 1495 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.33 % Allowed : 16.89 % Favored : 82.78 % 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 aren not related in a simple way. whole: 4.29 (0.25), residues: 1175 helix: 3.31 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.93 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 165 TYR 0.036 0.002 TYR E 159 PHE 0.004 0.001 PHE D 150 TRP 0.003 0.000 TRP A 75 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 9265) covalent geometry : angle 0.41755 (12505) hydrogen bonds : bond 0.03013 ( 843) hydrogen bonds : angle 3.11080 ( 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 113 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.369 Fit side-chains REVERT: A 52 MET cc_start: 0.7398 (mtp) cc_final: 0.6689 (mtm) REVERT: A 81 LYS cc_start: 0.8613 (ttpp) cc_final: 0.7968 (tptt) REVERT: B 52 MET cc_start: 0.7538 (mtp) cc_final: 0.6870 (mtm) REVERT: B 81 LYS cc_start: 0.8427 (ttpp) cc_final: 0.7764 (tptt) REVERT: B 159 TYR cc_start: 0.8019 (t80) cc_final: 0.7809 (t80) REVERT: B 204 LEU cc_start: 0.7746 (tt) cc_final: 0.7406 (tt) REVERT: C 52 MET cc_start: 0.7342 (mtp) cc_final: 0.6613 (mtm) REVERT: C 81 LYS cc_start: 0.8615 (ttpp) cc_final: 0.7901 (tptt) REVERT: C 113 GLN cc_start: 0.8295 (tp40) cc_final: 0.8089 (tp40) REVERT: C 130 ASN cc_start: 0.8498 (t0) cc_final: 0.8256 (t0) REVERT: C 252 GLN cc_start: 0.8333 (tt0) cc_final: 0.7825 (tt0) REVERT: D 52 MET cc_start: 0.7560 (mtp) cc_final: 0.6896 (mtm) REVERT: D 81 LYS cc_start: 0.8441 (ttpp) cc_final: 0.7895 (tptt) REVERT: D 126 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7366 (t0) REVERT: D 252 GLN cc_start: 0.8371 (tt0) cc_final: 0.7917 (tt0) REVERT: E 52 MET cc_start: 0.7370 (mtp) cc_final: 0.6661 (mtm) REVERT: E 81 LYS cc_start: 0.8533 (ttpp) cc_final: 0.7850 (tptt) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.0813 time to fit residues: 13.4987 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 0.0370 chunk 13 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116640 restraints weight = 28859.857| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.13 r_work: 0.3069 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2691 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= 0.116 Angle : 0.440 8.679 12505 Z= 0.227 Chirality : 0.034 0.125 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.401 58.128 1495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.44 % Allowed : 17.22 % Favored : 82.33 % 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 aren not related in a simple way. whole: 4.27 (0.24), residues: 1175 helix: 3.30 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.95 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 259 TYR 0.036 0.002 TYR E 159 PHE 0.005 0.001 PHE A 169 TRP 0.003 0.001 TRP A 75 HIS 0.002 0.000 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9265) covalent geometry : angle 0.44032 (12505) hydrogen bonds : bond 0.03081 ( 843) hydrogen bonds : angle 3.16041 ( 2524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.98 seconds wall clock time: 37 minutes 44.26 seconds (2264.26 seconds total)