Starting phenix.real_space_refine on Thu Feb 13 20:05:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ye4_10789/02_2025/6ye4_10789.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ye4_10789/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ye4_10789/02_2025/6ye4_10789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ye4_10789/02_2025/6ye4_10789.map" model { file = "/net/cci-nas-00/data/ceres_data/6ye4_10789/02_2025/6ye4_10789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ye4_10789/02_2025/6ye4_10789.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 9.70, per 1000 atoms: 1.06 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: 2.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 0.68 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: 2.61 Time building geometry restraints manager: 2.70 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- 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= 1.753 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.044 0.006 TRP C 50 HIS 0.023 0.004 HIS D 242 PHE 0.041 0.008 PHE D 79 TYR 0.023 0.008 TYR C 53 ARG 0.016 0.002 ARG B 154 *********************** 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 : 0.921 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: 0.2015 time to fit residues: 44.9686 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 : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 E 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111069 restraints weight = 40973.665| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.67 r_work: 0.2962 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1725 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= 0.225 Angle : 0.526 6.528 12505 Z= 0.273 Chirality : 0.035 0.149 1450 Planarity : 0.005 0.036 1605 Dihedral : 11.626 74.502 1495 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.11 % Allowed : 12.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 50 HIS 0.003 0.001 HIS C 242 PHE 0.008 0.002 PHE B 179 TYR 0.009 0.002 TYR D 159 ARG 0.002 0.000 ARG D 259 *********************** 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: 1 poor density : 111 time to evaluate : 0.850 Fit side-chains REVERT: A 52 MET cc_start: 0.7428 (mtp) cc_final: 0.6754 (mtt) REVERT: A 81 LYS cc_start: 0.8530 (ttpp) cc_final: 0.7770 (tptt) REVERT: A 96 GLN cc_start: 0.8778 (tt0) cc_final: 0.8531 (mt0) REVERT: A 133 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6535 (mt-10) REVERT: B 52 MET cc_start: 0.7609 (mtp) cc_final: 0.6823 (mtm) REVERT: B 81 LYS cc_start: 0.8406 (ttpp) cc_final: 0.7722 (tptt) REVERT: C 52 MET cc_start: 0.7451 (mtp) cc_final: 0.6637 (mtm) REVERT: C 81 LYS cc_start: 0.8525 (ttpp) cc_final: 0.7791 (tptt) REVERT: C 113 GLN cc_start: 0.8396 (tp40) cc_final: 0.8144 (tp40) REVERT: D 52 MET cc_start: 0.7535 (mtp) cc_final: 0.6852 (mtm) REVERT: D 81 LYS cc_start: 0.8487 (ttpp) cc_final: 0.7795 (tptt) REVERT: D 204 LEU cc_start: 0.7659 (tt) cc_final: 0.7301 (tt) REVERT: E 52 MET cc_start: 0.7494 (mtp) cc_final: 0.6881 (mtp) REVERT: E 81 LYS cc_start: 0.8567 (ttpp) cc_final: 0.7772 (tptt) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1920 time to fit residues: 30.7702 Evaluate side-chains 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.150528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112574 restraints weight = 28293.489| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.14 r_work: 0.2998 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2082 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= 0.212 Angle : 0.495 6.009 12505 Z= 0.259 Chirality : 0.035 0.141 1450 Planarity : 0.004 0.032 1605 Dihedral : 10.111 59.401 1495 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.67 % Allowed : 13.89 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1175 helix: 2.02 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.49 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 50 HIS 0.002 0.000 HIS C 242 PHE 0.007 0.001 PHE B 183 TYR 0.022 0.003 TYR A 159 ARG 0.003 0.000 ARG D 259 *********************** 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 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.963 Fit side-chains REVERT: A 52 MET cc_start: 0.7425 (mtp) cc_final: 0.6735 (mtt) REVERT: A 81 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7699 (tptt) REVERT: A 96 GLN cc_start: 0.8703 (tt0) cc_final: 0.8458 (mt0) REVERT: A 133 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6445 (mt-10) REVERT: B 52 MET cc_start: 0.7510 (mtp) cc_final: 0.6745 (mtm) REVERT: B 81 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7629 (tptt) REVERT: C 52 MET cc_start: 0.7333 (mtp) cc_final: 0.6552 (mtm) REVERT: C 81 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7689 (tptt) REVERT: C 113 GLN cc_start: 0.8400 (tp40) cc_final: 0.8147 (tp40) REVERT: D 52 MET cc_start: 0.7498 (mtp) cc_final: 0.6849 (mtm) REVERT: D 81 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7676 (tptt) REVERT: D 126 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7364 (t0) REVERT: E 52 MET cc_start: 0.7386 (mtp) cc_final: 0.6745 (mtp) REVERT: E 81 LYS cc_start: 0.8472 (ttpp) cc_final: 0.7648 (tptt) REVERT: E 159 TYR cc_start: 0.7862 (t80) cc_final: 0.7549 (t80) outliers start: 6 outliers final: 5 residues processed: 94 average time/residue: 0.1972 time to fit residues: 26.9657 Evaluate side-chains 93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 E residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 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 = 0.3677 r_free = 0.3677 target = 0.151527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113347 restraints weight = 30014.219| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.25 r_work: 0.3011 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2340 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= 0.179 Angle : 0.454 5.853 12505 Z= 0.236 Chirality : 0.034 0.126 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.899 50.485 1495 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.67 % Allowed : 14.44 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.25), residues: 1175 helix: 2.54 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.28 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 50 HIS 0.002 0.000 HIS D 242 PHE 0.006 0.001 PHE A 169 TYR 0.016 0.002 TYR B 159 ARG 0.002 0.000 ARG D 259 *********************** 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 104 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.835 Fit side-chains REVERT: A 52 MET cc_start: 0.7412 (mtp) cc_final: 0.6594 (mtm) REVERT: A 81 LYS cc_start: 0.8468 (ttpp) cc_final: 0.7808 (tptt) REVERT: A 96 GLN cc_start: 0.8672 (tt0) cc_final: 0.8450 (mt0) REVERT: A 133 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6411 (mt-10) REVERT: A 159 TYR cc_start: 0.7905 (t80) cc_final: 0.7679 (t80) REVERT: B 52 MET cc_start: 0.7465 (mtp) cc_final: 0.6724 (mtm) REVERT: B 81 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7638 (tptt) REVERT: C 52 MET cc_start: 0.7267 (mtp) cc_final: 0.6495 (mtm) REVERT: C 81 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7698 (tptt) REVERT: C 96 GLN cc_start: 0.8730 (mt0) cc_final: 0.8505 (mt0) REVERT: C 113 GLN cc_start: 0.8320 (tp40) cc_final: 0.8085 (tp40) REVERT: C 252 GLN cc_start: 0.8302 (tt0) cc_final: 0.7764 (tt0) REVERT: D 52 MET cc_start: 0.7450 (mtp) cc_final: 0.6802 (mtm) REVERT: D 81 LYS cc_start: 0.8391 (ttpp) cc_final: 0.7673 (tptt) REVERT: D 126 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7410 (t0) REVERT: E 52 MET cc_start: 0.7368 (mtp) cc_final: 0.6628 (mtm) REVERT: E 81 LYS cc_start: 0.8428 (ttpp) cc_final: 0.7630 (tptt) REVERT: E 160 SER cc_start: 0.8770 (p) cc_final: 0.8474 (m) outliers start: 6 outliers final: 5 residues processed: 99 average time/residue: 0.2062 time to fit residues: 29.7112 Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 E residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.150296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113400 restraints weight = 23321.021| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.83 r_work: 0.3026 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 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 = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2286 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= 0.216 Angle : 0.468 5.910 12505 Z= 0.242 Chirality : 0.035 0.119 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.909 52.790 1495 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.00 % Allowed : 15.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.25), residues: 1175 helix: 2.64 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.29 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.002 0.000 HIS E 242 PHE 0.007 0.001 PHE B 183 TYR 0.015 0.002 TYR C 159 ARG 0.003 0.000 ARG D 259 *********************** 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 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.955 Fit side-chains REVERT: A 52 MET cc_start: 0.7438 (mtp) cc_final: 0.6732 (mtt) REVERT: A 81 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7769 (tptt) REVERT: A 96 GLN cc_start: 0.8683 (tt0) cc_final: 0.8448 (mt0) REVERT: B 52 MET cc_start: 0.7579 (mtp) cc_final: 0.6782 (mtm) REVERT: B 81 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7669 (tptt) REVERT: B 159 TYR cc_start: 0.7818 (t80) cc_final: 0.7548 (t80) REVERT: C 52 MET cc_start: 0.7403 (mtp) cc_final: 0.6663 (mtm) REVERT: C 81 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7712 (tptt) REVERT: C 113 GLN cc_start: 0.8305 (tp40) cc_final: 0.8074 (tp40) REVERT: C 252 GLN cc_start: 0.8281 (tt0) cc_final: 0.7731 (tt0) REVERT: D 52 MET cc_start: 0.7534 (mtp) cc_final: 0.6870 (mtm) REVERT: D 81 LYS cc_start: 0.8420 (ttpp) cc_final: 0.7705 (tptt) REVERT: D 126 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7432 (t0) REVERT: E 52 MET cc_start: 0.7392 (mtp) cc_final: 0.6755 (mtp) REVERT: E 81 LYS cc_start: 0.8454 (ttpp) cc_final: 0.7661 (tptt) REVERT: E 160 SER cc_start: 0.8726 (p) cc_final: 0.8444 (m) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.1917 time to fit residues: 25.9631 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 : 1.056 ------------------------------------------------------------------------------- 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 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 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.151197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112451 restraints weight = 32858.367| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.41 r_work: 0.2976 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2393 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= 0.190 Angle : 0.449 5.856 12505 Z= 0.233 Chirality : 0.034 0.115 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.731 56.152 1495 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 15.00 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.25), residues: 1175 helix: 2.83 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.23 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 50 HIS 0.002 0.000 HIS D 242 PHE 0.006 0.001 PHE E 169 TYR 0.015 0.002 TYR C 159 ARG 0.002 0.000 ARG D 259 *********************** 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: 7 poor density : 92 time to evaluate : 1.011 Fit side-chains REVERT: A 52 MET cc_start: 0.7403 (mtp) cc_final: 0.6690 (mtt) REVERT: A 81 LYS cc_start: 0.8493 (ttpp) cc_final: 0.7840 (tptt) REVERT: A 96 GLN cc_start: 0.8674 (tt0) cc_final: 0.8453 (mt0) REVERT: B 52 MET cc_start: 0.7510 (mtp) cc_final: 0.6743 (mtm) REVERT: B 81 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7660 (tptt) REVERT: B 159 TYR cc_start: 0.7844 (t80) cc_final: 0.7580 (t80) REVERT: C 52 MET cc_start: 0.7347 (mtp) cc_final: 0.6581 (mtm) REVERT: C 81 LYS cc_start: 0.8464 (ttpp) cc_final: 0.7730 (tptt) REVERT: C 113 GLN cc_start: 0.8308 (tp40) cc_final: 0.8088 (tp40) REVERT: C 252 GLN cc_start: 0.8338 (tt0) cc_final: 0.7797 (tt0) REVERT: D 52 MET cc_start: 0.7514 (mtp) cc_final: 0.6836 (mtm) REVERT: D 81 LYS cc_start: 0.8401 (ttpp) cc_final: 0.7769 (tptt) REVERT: D 113 GLN cc_start: 0.8303 (tp40) cc_final: 0.8065 (mm-40) REVERT: D 126 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7421 (t0) REVERT: E 52 MET cc_start: 0.7323 (mtp) cc_final: 0.6690 (mtp) REVERT: E 81 LYS cc_start: 0.8436 (ttpp) cc_final: 0.7677 (tptt) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.1953 time to fit residues: 27.0769 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 : 0.928 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 130 ASN E 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111789 restraints weight = 28895.037| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.20 r_work: 0.2993 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2340 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= 0.219 Angle : 0.462 5.904 12505 Z= 0.238 Chirality : 0.035 0.115 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.888 59.016 1495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.24), residues: 1175 helix: 2.82 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.18 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.002 0.000 HIS B 242 PHE 0.007 0.001 PHE B 183 TYR 0.016 0.002 TYR A 159 ARG 0.002 0.000 ARG D 259 *********************** 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 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.035 Fit side-chains REVERT: A 52 MET cc_start: 0.7392 (mtp) cc_final: 0.6692 (mtt) REVERT: A 81 LYS cc_start: 0.8490 (ttpp) cc_final: 0.7764 (tptt) REVERT: A 96 GLN cc_start: 0.8672 (tt0) cc_final: 0.8427 (mt0) REVERT: B 52 MET cc_start: 0.7554 (mtp) cc_final: 0.6754 (mtm) REVERT: B 81 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7651 (tptt) REVERT: C 52 MET cc_start: 0.7369 (mtp) cc_final: 0.6624 (mtm) REVERT: C 81 LYS cc_start: 0.8439 (ttpp) cc_final: 0.7700 (tptt) REVERT: C 113 GLN cc_start: 0.8285 (tp40) cc_final: 0.8061 (tp40) REVERT: C 252 GLN cc_start: 0.8299 (tt0) cc_final: 0.7749 (tt0) REVERT: D 52 MET cc_start: 0.7523 (mtp) cc_final: 0.6854 (mtm) REVERT: D 81 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7766 (tptt) REVERT: D 113 GLN cc_start: 0.8367 (tp40) cc_final: 0.8141 (mm-40) REVERT: D 126 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7427 (t0) REVERT: E 52 MET cc_start: 0.7338 (mtp) cc_final: 0.6682 (mtp) REVERT: E 81 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7679 (tptt) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1962 time to fit residues: 26.8388 Evaluate side-chains 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 192 SER Chi-restraints excluded: chain D residue 126 ASN 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 38 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.150143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111982 restraints weight = 28637.905| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.18 r_work: 0.2994 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 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 = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2359 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= 0.223 Angle : 0.466 5.904 12505 Z= 0.241 Chirality : 0.035 0.113 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.933 59.483 1495 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.00 % Allowed : 15.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.24), residues: 1175 helix: 2.87 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.11 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.003 0.000 HIS B 242 PHE 0.007 0.001 PHE B 183 TYR 0.016 0.002 TYR C 159 ARG 0.002 0.000 ARG D 259 *********************** 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 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.926 Fit side-chains REVERT: A 52 MET cc_start: 0.7434 (mtp) cc_final: 0.6706 (mtt) REVERT: A 81 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7777 (tptt) REVERT: A 96 GLN cc_start: 0.8696 (tt0) cc_final: 0.8443 (mt0) REVERT: B 52 MET cc_start: 0.7557 (mtp) cc_final: 0.6736 (mtm) REVERT: B 81 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7669 (tptt) REVERT: C 52 MET cc_start: 0.7357 (mtp) cc_final: 0.6612 (mtm) REVERT: C 81 LYS cc_start: 0.8447 (ttpp) cc_final: 0.7707 (tptt) REVERT: C 113 GLN cc_start: 0.8304 (tp40) cc_final: 0.8083 (tp40) REVERT: C 252 GLN cc_start: 0.8322 (tt0) cc_final: 0.7772 (tt0) REVERT: D 52 MET cc_start: 0.7526 (mtp) cc_final: 0.6855 (mtm) REVERT: D 81 LYS cc_start: 0.8416 (ttpp) cc_final: 0.7780 (tptt) REVERT: D 113 GLN cc_start: 0.8347 (tp40) cc_final: 0.8145 (mm-40) REVERT: D 126 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7436 (t0) REVERT: E 52 MET cc_start: 0.7361 (mtp) cc_final: 0.6702 (mtp) REVERT: E 81 LYS cc_start: 0.8473 (ttpp) cc_final: 0.7676 (tptt) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.1913 time to fit residues: 25.3407 Evaluate side-chains 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 110 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.153180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115942 restraints weight = 25912.784| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.04 r_work: 0.3060 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2629 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= 0.143 Angle : 0.422 5.726 12505 Z= 0.220 Chirality : 0.033 0.110 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.472 59.861 1495 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.78 % Allowed : 15.78 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.24), residues: 1175 helix: 3.18 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.99 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 75 HIS 0.002 0.000 HIS D 242 PHE 0.005 0.001 PHE E 169 TYR 0.032 0.002 TYR E 159 ARG 0.001 0.000 ARG A 165 *********************** 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 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.010 Fit side-chains REVERT: A 52 MET cc_start: 0.7306 (mtp) cc_final: 0.6560 (mtm) REVERT: A 81 LYS cc_start: 0.8432 (ttpp) cc_final: 0.7817 (tptt) REVERT: B 52 MET cc_start: 0.7465 (mtp) cc_final: 0.6792 (mtm) REVERT: B 81 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7600 (tptt) REVERT: B 159 TYR cc_start: 0.7870 (t80) cc_final: 0.7656 (t80) REVERT: B 204 LEU cc_start: 0.7630 (tt) cc_final: 0.7301 (tt) REVERT: C 52 MET cc_start: 0.7231 (mtp) cc_final: 0.6537 (mtm) REVERT: C 81 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7748 (tptt) REVERT: C 113 GLN cc_start: 0.8229 (tp40) cc_final: 0.8023 (tp40) REVERT: C 252 GLN cc_start: 0.8303 (tt0) cc_final: 0.7773 (tt0) REVERT: D 52 MET cc_start: 0.7466 (mtp) cc_final: 0.6798 (mtm) REVERT: D 81 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7775 (tptt) REVERT: D 113 GLN cc_start: 0.8322 (tp40) cc_final: 0.8116 (mm-40) REVERT: D 126 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7336 (t0) REVERT: D 159 TYR cc_start: 0.7733 (t80) cc_final: 0.7388 (t80) REVERT: D 252 GLN cc_start: 0.8299 (tt0) cc_final: 0.7831 (tt0) REVERT: E 52 MET cc_start: 0.7302 (mtp) cc_final: 0.6584 (mtm) REVERT: E 81 LYS cc_start: 0.8379 (ttpp) cc_final: 0.7776 (tptt) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.1811 time to fit residues: 28.3381 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 : 0.901 ------------------------------------------------------------------------------- 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 D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER 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 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114873 restraints weight = 25255.840| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.97 r_work: 0.3040 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 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 = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2605 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= 0.174 Angle : 0.443 8.989 12505 Z= 0.227 Chirality : 0.034 0.111 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.533 59.268 1495 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.89 % Allowed : 16.22 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.24), residues: 1175 helix: 3.18 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.99 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 75 HIS 0.002 0.000 HIS D 242 PHE 0.005 0.001 PHE A 169 TYR 0.036 0.002 TYR E 159 ARG 0.001 0.000 ARG D 259 ********************** 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 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.027 Fit side-chains REVERT: A 52 MET cc_start: 0.7444 (mtp) cc_final: 0.6662 (mtm) REVERT: A 81 LYS cc_start: 0.8502 (ttpp) cc_final: 0.7892 (tptt) REVERT: B 52 MET cc_start: 0.7541 (mtp) cc_final: 0.6850 (mtm) REVERT: B 81 LYS cc_start: 0.8375 (ttpp) cc_final: 0.7732 (tptt) REVERT: B 204 LEU cc_start: 0.7694 (tt) cc_final: 0.7377 (tt) REVERT: C 52 MET cc_start: 0.7336 (mtp) cc_final: 0.6620 (mtm) REVERT: C 81 LYS cc_start: 0.8487 (ttpp) cc_final: 0.7781 (tptt) REVERT: C 113 GLN cc_start: 0.8232 (tp40) cc_final: 0.8028 (tp40) REVERT: C 252 GLN cc_start: 0.8334 (tt0) cc_final: 0.7808 (tt0) REVERT: D 52 MET cc_start: 0.7490 (mtp) cc_final: 0.6871 (mtm) REVERT: D 81 LYS cc_start: 0.8427 (ttpp) cc_final: 0.7834 (tptt) REVERT: D 126 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7350 (t0) REVERT: D 159 TYR cc_start: 0.7784 (t80) cc_final: 0.7432 (t80) REVERT: D 252 GLN cc_start: 0.8324 (tt0) cc_final: 0.7855 (tt0) REVERT: E 52 MET cc_start: 0.7411 (mtp) cc_final: 0.6733 (mtp) REVERT: E 81 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7820 (tptt) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.1847 time to fit residues: 26.9689 Evaluate side-chains 104 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 D residue 126 ASN 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 92 optimal weight: 0.0060 chunk 57 optimal weight: 0.0570 chunk 81 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 37 optimal weight: 0.6980 overall best weight: 0.3012 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.154995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117707 restraints weight = 31579.196| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.29 r_work: 0.3078 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 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 = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9265 Z= 0.134 Angle : 0.423 8.250 12505 Z= 0.219 Chirality : 0.033 0.109 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.331 58.568 1495 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.44 % Allowed : 16.67 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.24), residues: 1175 helix: 3.35 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.90 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 75 HIS 0.003 0.000 HIS B 242 PHE 0.004 0.001 PHE A 169 TYR 0.036 0.002 TYR E 159 ARG 0.001 0.000 ARG D 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.53 seconds wall clock time: 71 minutes 37.76 seconds (4297.76 seconds total)