Starting phenix.real_space_refine on Wed Sep 25 02:42:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ye4_10789/09_2024/6ye4_10789.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ye4_10789/09_2024/6ye4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ye4_10789/09_2024/6ye4_10789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ye4_10789/09_2024/6ye4_10789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ye4_10789/09_2024/6ye4_10789.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ye4_10789/09_2024/6ye4_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-5461/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: 10.47, per 1000 atoms: 1.15 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: 2.14 Conformation dependent library (CDL) restraints added in 2.0 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: 0.64 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: 2.55 Time building geometry restraints manager: 2.52 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 160 or resid 162 through 281 or resid 301)) selection = (chain 'B' and (resid 46 through 160 or resid 162 through 281 or resid 301)) selection = (chain 'C' and (resid 46 through 160 or resid 162 through 281 or resid 301)) selection = (chain 'D' and (resid 46 through 160 or resid 162 through 281 or resid 301)) selection = (chain 'E' and (resid 46 through 160 or resid 162 through 281 or resid 301)) } 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: 9.380 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.460 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.974 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: 0.1933 time to fit residues: 43.1974 Evaluate side-chains 107 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.896 Fit side-chains REVERT: A 52 MET cc_start: 0.7890 (mtp) cc_final: 0.7330 (mtt) REVERT: A 81 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8188 (tptt) REVERT: A 96 GLN cc_start: 0.8822 (tt0) cc_final: 0.8617 (mt0) REVERT: B 52 MET cc_start: 0.7922 (mtp) cc_final: 0.7445 (mtm) REVERT: B 81 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8226 (tptt) REVERT: C 52 MET cc_start: 0.7865 (mtp) cc_final: 0.7210 (mtm) REVERT: C 81 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8238 (tptt) REVERT: D 52 MET cc_start: 0.7893 (mtp) cc_final: 0.7399 (mtm) REVERT: D 81 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8203 (tptt) REVERT: D 204 LEU cc_start: 0.8124 (tt) cc_final: 0.7858 (tt) REVERT: E 52 MET cc_start: 0.7913 (mtp) cc_final: 0.7424 (mtp) REVERT: E 81 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8258 (tptt) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1889 time to fit residues: 30.2483 Evaluate side-chains 93 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2117 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= 0.208 Angle : 0.491 5.961 12505 Z= 0.257 Chirality : 0.035 0.138 1450 Planarity : 0.004 0.032 1605 Dihedral : 9.995 58.283 1495 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.67 % Allowed : 14.00 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.34 (0.24), residues: 1175 helix: 2.03 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.46 (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 0.002 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 97 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.919 Fit side-chains REVERT: A 52 MET cc_start: 0.7875 (mtp) cc_final: 0.7310 (mtt) REVERT: A 81 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8171 (tptt) REVERT: B 52 MET cc_start: 0.7876 (mtp) cc_final: 0.7421 (mtm) REVERT: B 81 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8232 (tptt) REVERT: B 160 SER cc_start: 0.9086 (p) cc_final: 0.8881 (m) REVERT: C 52 MET cc_start: 0.7843 (mtp) cc_final: 0.7270 (mtm) REVERT: C 81 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8200 (tptt) REVERT: D 52 MET cc_start: 0.7899 (mtp) cc_final: 0.7467 (mtm) REVERT: D 81 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8185 (tptt) REVERT: E 52 MET cc_start: 0.7884 (mtp) cc_final: 0.7373 (mtp) REVERT: E 81 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8233 (tptt) outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.1922 time to fit residues: 26.0639 Evaluate side-chains 95 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 103 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2263 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= 0.201 Angle : 0.465 5.900 12505 Z= 0.241 Chirality : 0.034 0.125 1450 Planarity : 0.003 0.031 1605 Dihedral : 9.059 49.757 1495 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.56 % Allowed : 14.56 % 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: 3.00 (0.25), residues: 1175 helix: 2.47 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.32 (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 D 242 PHE 0.006 0.001 PHE A 183 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 95 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.910 Fit side-chains REVERT: A 52 MET cc_start: 0.7844 (mtp) cc_final: 0.7281 (mtt) REVERT: A 81 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8216 (tptt) REVERT: B 52 MET cc_start: 0.7875 (mtp) cc_final: 0.7411 (mtm) REVERT: B 81 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8245 (tptt) REVERT: C 52 MET cc_start: 0.7813 (mtp) cc_final: 0.7265 (mtm) REVERT: C 81 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8166 (tptt) REVERT: C 252 GLN cc_start: 0.7906 (tt0) cc_final: 0.7553 (tt0) REVERT: D 52 MET cc_start: 0.7867 (mtp) cc_final: 0.7449 (mtm) REVERT: D 81 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8192 (tptt) REVERT: E 52 MET cc_start: 0.7849 (mtp) cc_final: 0.7364 (mtp) REVERT: E 81 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8253 (tptt) outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.1840 time to fit residues: 24.5608 Evaluate side-chains 90 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9265 Z= 0.156 Angle : 0.434 5.774 12505 Z= 0.225 Chirality : 0.033 0.117 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.454 53.782 1495 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 14.78 % 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 (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: 3.58 (0.25), residues: 1175 helix: 2.85 (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 0.003 0.001 TRP A 75 HIS 0.002 0.000 HIS D 242 PHE 0.005 0.001 PHE E 169 TYR 0.022 0.002 TYR A 159 ARG 0.002 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 114 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.783 Fit side-chains REVERT: A 52 MET cc_start: 0.7816 (mtp) cc_final: 0.7283 (mtm) REVERT: A 81 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8303 (tptt) REVERT: B 52 MET cc_start: 0.7831 (mtp) cc_final: 0.7434 (mtm) REVERT: B 81 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8266 (tptt) REVERT: C 52 MET cc_start: 0.7718 (mtp) cc_final: 0.7175 (mtm) REVERT: C 81 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8226 (tptt) REVERT: C 252 GLN cc_start: 0.7897 (tt0) cc_final: 0.7548 (tt0) REVERT: D 52 MET cc_start: 0.7818 (mtp) cc_final: 0.7429 (mtm) REVERT: D 81 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8260 (tptt) REVERT: D 252 GLN cc_start: 0.7911 (tt0) cc_final: 0.7586 (tt0) REVERT: E 52 MET cc_start: 0.7798 (mtp) cc_final: 0.7291 (mtm) REVERT: E 81 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8243 (tptt) outliers start: 7 outliers final: 5 residues processed: 109 average time/residue: 0.1788 time to fit residues: 28.9319 Evaluate side-chains 99 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 D residue 192 SER Chi-restraints excluded: chain E residue 153 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9265 Z= 0.164 Angle : 0.437 5.785 12505 Z= 0.226 Chirality : 0.034 0.114 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.498 56.718 1495 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.78 % Allowed : 15.33 % 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: 3.81 (0.25), residues: 1175 helix: 3.01 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.17 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 75 HIS 0.002 0.000 HIS B 242 PHE 0.005 0.001 PHE E 169 TYR 0.029 0.002 TYR A 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 102 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.926 Fit side-chains REVERT: A 52 MET cc_start: 0.7829 (mtp) cc_final: 0.7292 (mtm) REVERT: A 81 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8227 (tptt) REVERT: B 52 MET cc_start: 0.7838 (mtp) cc_final: 0.7431 (mtm) REVERT: B 81 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8268 (tptt) REVERT: C 52 MET cc_start: 0.7721 (mtp) cc_final: 0.7170 (mtm) REVERT: C 81 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8209 (tptt) REVERT: C 252 GLN cc_start: 0.7894 (tt0) cc_final: 0.7544 (tt0) REVERT: D 52 MET cc_start: 0.7857 (mtp) cc_final: 0.7442 (mtm) REVERT: D 81 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8258 (tptt) REVERT: D 252 GLN cc_start: 0.7909 (tt0) cc_final: 0.7564 (tt0) REVERT: E 52 MET cc_start: 0.7810 (mtp) cc_final: 0.7302 (mtm) REVERT: E 81 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8253 (tptt) outliers start: 7 outliers final: 7 residues processed: 95 average time/residue: 0.1964 time to fit residues: 27.4056 Evaluate side-chains 100 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 69 optimal weight: 0.0670 chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2615 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= 0.163 Angle : 0.433 5.770 12505 Z= 0.225 Chirality : 0.034 0.113 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.478 59.398 1495 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.00 % Allowed : 15.78 % 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 (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: 3.97 (0.25), residues: 1175 helix: 3.11 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.08 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 75 HIS 0.002 0.000 HIS B 242 PHE 0.005 0.001 PHE E 169 TYR 0.026 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 104 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.082 Fit side-chains REVERT: A 52 MET cc_start: 0.7786 (mtp) cc_final: 0.7252 (mtm) REVERT: A 81 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8312 (tptt) REVERT: B 52 MET cc_start: 0.7829 (mtp) cc_final: 0.7433 (mtm) REVERT: B 81 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8194 (tptt) REVERT: C 52 MET cc_start: 0.7699 (mtp) cc_final: 0.7175 (mtm) REVERT: C 81 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8240 (tptt) REVERT: C 252 GLN cc_start: 0.7889 (tt0) cc_final: 0.7541 (tt0) REVERT: D 52 MET cc_start: 0.7834 (mtp) cc_final: 0.7446 (mtm) REVERT: D 81 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8257 (tptt) REVERT: D 252 GLN cc_start: 0.7908 (tt0) cc_final: 0.7564 (tt0) REVERT: E 52 MET cc_start: 0.7791 (mtp) cc_final: 0.7289 (mtm) REVERT: E 81 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8260 (tptt) outliers start: 9 outliers final: 9 residues processed: 95 average time/residue: 0.1887 time to fit residues: 26.4246 Evaluate side-chains 103 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2514 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= 0.194 Angle : 0.449 5.832 12505 Z= 0.233 Chirality : 0.035 0.113 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.680 59.740 1495 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.11 % Allowed : 15.56 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.90 (0.24), residues: 1175 helix: 3.05 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.03 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.002 0.000 HIS B 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 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 103 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.973 Fit side-chains REVERT: A 52 MET cc_start: 0.7825 (mtp) cc_final: 0.7261 (mtt) REVERT: A 81 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8235 (tptt) REVERT: B 52 MET cc_start: 0.7858 (mtp) cc_final: 0.7414 (mtm) REVERT: B 81 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8270 (tptt) REVERT: C 52 MET cc_start: 0.7749 (mtp) cc_final: 0.7216 (mtm) REVERT: C 81 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8207 (tptt) REVERT: C 252 GLN cc_start: 0.7892 (tt0) cc_final: 0.7534 (tt0) REVERT: D 52 MET cc_start: 0.7867 (mtp) cc_final: 0.7441 (mtm) REVERT: D 81 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8270 (tptt) REVERT: E 52 MET cc_start: 0.7834 (mtp) cc_final: 0.7301 (mtp) REVERT: E 81 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8266 (tptt) outliers start: 10 outliers final: 10 residues processed: 93 average time/residue: 0.1909 time to fit residues: 26.0842 Evaluate side-chains 103 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain 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 103 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2527 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= 0.194 Angle : 0.446 5.837 12505 Z= 0.231 Chirality : 0.034 0.112 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.645 59.009 1495 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.00 % Allowed : 15.78 % 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 (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: 3.95 (0.24), residues: 1175 helix: 3.09 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.98 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 50 HIS 0.002 0.000 HIS B 242 PHE 0.006 0.001 PHE E 169 TYR 0.020 0.002 TYR A 159 ARG 0.002 0.000 ARG D 259 *********************** 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 101 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.023 Fit side-chains REVERT: A 52 MET cc_start: 0.7813 (mtp) cc_final: 0.7257 (mtm) REVERT: A 81 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8240 (tptt) REVERT: B 52 MET cc_start: 0.7846 (mtp) cc_final: 0.7402 (mtm) REVERT: B 81 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8279 (tptt) REVERT: B 204 LEU cc_start: 0.8067 (tt) cc_final: 0.7822 (tt) REVERT: C 52 MET cc_start: 0.7736 (mtp) cc_final: 0.7203 (mtm) REVERT: C 81 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8235 (tptt) REVERT: C 252 GLN cc_start: 0.7890 (tt0) cc_final: 0.7532 (tt0) REVERT: D 52 MET cc_start: 0.7853 (mtp) cc_final: 0.7426 (mtm) REVERT: D 81 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8269 (tptt) REVERT: E 52 MET cc_start: 0.7836 (mtp) cc_final: 0.7314 (mtp) REVERT: E 81 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8253 (tptt) outliers start: 9 outliers final: 9 residues processed: 92 average time/residue: 0.1938 time to fit residues: 26.0977 Evaluate side-chains 101 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2462 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= 0.219 Angle : 0.458 5.894 12505 Z= 0.237 Chirality : 0.035 0.113 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.734 58.511 1495 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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 (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: 3.90 (0.24), residues: 1175 helix: 3.05 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.97 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.002 0.000 HIS C 242 PHE 0.007 0.001 PHE E 183 TYR 0.017 0.002 TYR E 159 ARG 0.002 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 102 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.937 Fit side-chains REVERT: A 52 MET cc_start: 0.7831 (mtp) cc_final: 0.7287 (mtm) REVERT: A 81 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8240 (tptt) REVERT: B 52 MET cc_start: 0.7864 (mtp) cc_final: 0.7388 (mtm) REVERT: B 81 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8272 (tptt) REVERT: B 204 LEU cc_start: 0.8076 (tt) cc_final: 0.7826 (tt) REVERT: C 52 MET cc_start: 0.7761 (mtp) cc_final: 0.7216 (mtm) REVERT: C 81 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8224 (tptt) REVERT: C 252 GLN cc_start: 0.7917 (tt0) cc_final: 0.7547 (tt0) REVERT: D 52 MET cc_start: 0.7876 (mtp) cc_final: 0.7436 (mtm) REVERT: D 81 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8281 (tptt) REVERT: E 52 MET cc_start: 0.7799 (mtp) cc_final: 0.7306 (mtp) REVERT: E 81 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8270 (tptt) outliers start: 9 outliers final: 9 residues processed: 93 average time/residue: 0.1961 time to fit residues: 26.9294 Evaluate side-chains 101 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 0.0270 chunk 84 optimal weight: 0.0170 chunk 13 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117490 restraints weight = 16891.572| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.37 r_work: 0.3091 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2579 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= 0.169 Angle : 0.434 5.779 12505 Z= 0.226 Chirality : 0.034 0.111 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.568 57.903 1495 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.89 % Allowed : 16.00 % 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 (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: 4.11 (0.24), residues: 1175 helix: 3.19 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.87 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 50 HIS 0.002 0.000 HIS B 242 PHE 0.005 0.001 PHE E 169 TYR 0.015 0.002 TYR C 159 ARG 0.002 0.000 ARG D 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.62 seconds wall clock time: 34 minutes 2.86 seconds (2042.86 seconds total)