Starting phenix.real_space_refine on Fri Jul 3 18:11:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyi_47305/07_2026/9dyi_47305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyi_47305/07_2026/9dyi_47305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dyi_47305/07_2026/9dyi_47305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyi_47305/07_2026/9dyi_47305.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyi_47305/07_2026/9dyi_47305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyi_47305/07_2026/9dyi_47305.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.082 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 85 5.16 5 Cl 1 4.86 5 C 10145 2.51 5 N 2560 2.21 5 O 2725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15521 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 3093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3167 Chain: "D" Number of atoms: 3093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3167 Chain: "A" Number of atoms: 3093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3167 Chain: "C" Number of atoms: 3093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3167 Chain: "B" Number of atoms: 3093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3167 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Chain breaks: 2 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 6.19, per 1000 atoms: 0.40 Number of scatterers: 15521 At special positions: 0 Unit cell: (104.775, 106.425, 110.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 85 16.00 O 2725 8.00 N 2560 7.00 C 10145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 70.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.545A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.582A pdb=" N GLN E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.967A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.728A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.544A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.582A pdb=" N GLN D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.967A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.728A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.545A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.582A pdb=" N GLN A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.967A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.728A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.545A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.582A pdb=" N GLN C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.967A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.728A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.545A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.582A pdb=" N GLN B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.967A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.727A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 371 through 375 985 hydrogen bonds defined for protein. 2815 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: 2.44 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2440 1.30 - 1.43: 4755 1.43 - 1.56: 8605 1.56 - 1.69: 0 1.69 - 1.82: 130 Bond restraints: 15930 Sorted by residual: bond pdb=" C ASN C 179 " pdb=" O ASN C 179 " ideal model delta sigma weight residual 1.234 1.297 -0.063 1.22e-02 6.72e+03 2.70e+01 bond pdb=" C ASN B 179 " pdb=" O ASN B 179 " ideal model delta sigma weight residual 1.234 1.297 -0.063 1.22e-02 6.72e+03 2.66e+01 bond pdb=" C ASN A 179 " pdb=" O ASN A 179 " ideal model delta sigma weight residual 1.234 1.297 -0.063 1.22e-02 6.72e+03 2.66e+01 bond pdb=" C ASN E 179 " pdb=" O ASN E 179 " ideal model delta sigma weight residual 1.234 1.297 -0.063 1.22e-02 6.72e+03 2.65e+01 bond pdb=" C ASN D 179 " pdb=" O ASN D 179 " ideal model delta sigma weight residual 1.234 1.297 -0.063 1.22e-02 6.72e+03 2.64e+01 ... (remaining 15925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 15077 1.75 - 3.50: 5631 3.50 - 5.26: 838 5.26 - 7.01: 64 7.01 - 8.76: 15 Bond angle restraints: 21625 Sorted by residual: angle pdb=" N ARG A 130 " pdb=" CA ARG A 130 " pdb=" C ARG A 130 " ideal model delta sigma weight residual 111.36 102.60 8.76 1.09e+00 8.42e-01 6.46e+01 angle pdb=" N ARG E 130 " pdb=" CA ARG E 130 " pdb=" C ARG E 130 " ideal model delta sigma weight residual 111.36 102.62 8.74 1.09e+00 8.42e-01 6.43e+01 angle pdb=" N ARG C 130 " pdb=" CA ARG C 130 " pdb=" C ARG C 130 " ideal model delta sigma weight residual 111.36 102.65 8.71 1.09e+00 8.42e-01 6.39e+01 angle pdb=" N ARG D 130 " pdb=" CA ARG D 130 " pdb=" C ARG D 130 " ideal model delta sigma weight residual 111.36 102.66 8.70 1.09e+00 8.42e-01 6.37e+01 angle pdb=" N ARG B 130 " pdb=" CA ARG B 130 " pdb=" C ARG B 130 " ideal model delta sigma weight residual 111.36 102.67 8.69 1.09e+00 8.42e-01 6.36e+01 ... (remaining 21620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 8430 17.74 - 35.48: 670 35.48 - 53.23: 130 53.23 - 70.97: 40 70.97 - 88.71: 15 Dihedral angle restraints: 9285 sinusoidal: 3700 harmonic: 5585 Sorted by residual: dihedral pdb=" CA LEU B 329 " pdb=" C LEU B 329 " pdb=" N ALA B 330 " pdb=" CA ALA B 330 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU D 329 " pdb=" C LEU D 329 " pdb=" N ALA D 330 " pdb=" CA ALA D 330 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU E 329 " pdb=" C LEU E 329 " pdb=" N ALA E 330 " pdb=" CA ALA E 330 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1171 0.050 - 0.101: 748 0.101 - 0.151: 311 0.151 - 0.202: 105 0.202 - 0.252: 15 Chirality restraints: 2350 Sorted by residual: chirality pdb=" CB ILE A 295 " pdb=" CA ILE A 295 " pdb=" CG1 ILE A 295 " pdb=" CG2 ILE A 295 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE D 295 " pdb=" CA ILE D 295 " pdb=" CG1 ILE D 295 " pdb=" CG2 ILE D 295 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE B 295 " pdb=" CA ILE B 295 " pdb=" CG1 ILE B 295 " pdb=" CG2 ILE B 295 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2347 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 182 " -0.075 2.00e-02 2.50e+03 3.69e-02 3.40e+01 pdb=" CG TRP A 182 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 182 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 182 " 0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP A 182 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 182 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 182 " 0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 182 " -0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 182 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 182 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 182 " -0.075 2.00e-02 2.50e+03 3.68e-02 3.39e+01 pdb=" CG TRP D 182 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP D 182 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 182 " 0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP D 182 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP D 182 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP D 182 " 0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 182 " -0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 182 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP D 182 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 182 " 0.075 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP B 182 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 182 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 182 " -0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP B 182 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 182 " 0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 182 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 182 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 182 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 182 " 0.046 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1700 2.75 - 3.29: 16956 3.29 - 3.83: 27509 3.83 - 4.36: 36450 4.36 - 4.90: 57772 Nonbonded interactions: 140387 Sorted by model distance: nonbonded pdb=" OH TYR A 43 " pdb=" O ARG A 255 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR D 43 " pdb=" O ARG D 255 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR E 43 " pdb=" O ARG E 255 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 43 " pdb=" O ARG C 255 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 43 " pdb=" O ARG B 255 " model vdw 2.219 3.040 ... (remaining 140382 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 2 through 239 or resid 241 through 602)) selection = (chain 'B' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'C' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'D' and (resid 2 through 239 or resid 241 through 602)) selection = (chain 'E' and (resid 2 through 239 or resid 241 through 602)) } 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.690 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.014 0.063 15930 Z= 1.022 Angle : 1.710 8.762 21625 Z= 1.271 Chirality : 0.077 0.252 2350 Planarity : 0.010 0.041 2730 Dihedral : 14.282 88.709 5695 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.22 % Allowed : 2.13 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 1875 helix: -0.02 (0.13), residues: 1290 sheet: None (None), residues: 0 loop : -0.75 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG C 126 TYR 0.075 0.013 TYR A 97 PHE 0.055 0.011 PHE C 148 TRP 0.075 0.013 TRP B 182 HIS 0.016 0.007 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.01435 / 1.02 (15930) covalent geometry : angle 1.70974 / 1.27 (21625) hydrogen bonds : bond 0.14675 / 9.86 ( 985) hydrogen bonds : angle 6.20100 / 4.48 ( 2815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.589 Fit side-chains REVERT: E 13 ARG cc_start: 0.6489 (mtp-110) cc_final: 0.6218 (mtm110) REVERT: E 59 LYS cc_start: 0.6121 (mtpt) cc_final: 0.5802 (mttp) REVERT: E 70 ASP cc_start: 0.7706 (t70) cc_final: 0.7407 (t0) REVERT: E 117 ARG cc_start: 0.8327 (mtp180) cc_final: 0.8105 (mtp180) REVERT: E 168 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.6571 (ttp-170) REVERT: E 189 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8153 (m) REVERT: E 223 MET cc_start: 0.8075 (mmm) cc_final: 0.7641 (mmt) REVERT: E 347 TYR cc_start: 0.6056 (m-80) cc_final: 0.5839 (m-80) REVERT: E 354 GLN cc_start: 0.6041 (OUTLIER) cc_final: 0.5013 (mt0) REVERT: D 13 ARG cc_start: 0.6514 (mtp-110) cc_final: 0.6206 (mtm110) REVERT: D 117 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7656 (tpp80) REVERT: D 168 ARG cc_start: 0.7150 (ttt-90) cc_final: 0.6372 (ttp-170) REVERT: D 319 MET cc_start: 0.8236 (mmt) cc_final: 0.7598 (mmt) REVERT: D 354 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5221 (mt0) REVERT: A 13 ARG cc_start: 0.6662 (mtp-110) cc_final: 0.6378 (mtm110) REVERT: A 70 ASP cc_start: 0.7923 (t70) cc_final: 0.7667 (t0) REVERT: A 168 ARG cc_start: 0.7166 (ttt-90) cc_final: 0.6400 (ttp-170) REVERT: A 223 MET cc_start: 0.8129 (mmm) cc_final: 0.7685 (mmt) REVERT: A 319 MET cc_start: 0.8049 (mmt) cc_final: 0.7749 (mmm) REVERT: A 354 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.5680 (mt0) REVERT: C 70 ASP cc_start: 0.8034 (t70) cc_final: 0.7715 (t0) REVERT: C 117 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7891 (mtp180) REVERT: C 168 ARG cc_start: 0.7053 (ttt-90) cc_final: 0.6240 (ttp-170) REVERT: C 172 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 319 MET cc_start: 0.8218 (mmt) cc_final: 0.7950 (mmm) REVERT: C 354 GLN cc_start: 0.5503 (OUTLIER) cc_final: 0.5213 (mt0) REVERT: B 70 ASP cc_start: 0.7783 (t70) cc_final: 0.7421 (t0) REVERT: B 168 ARG cc_start: 0.6968 (ttt-90) cc_final: 0.6243 (ttp-170) REVERT: B 174 LEU cc_start: 0.7686 (mp) cc_final: 0.7452 (mt) REVERT: B 316 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8406 (tt0) REVERT: B 324 GLU cc_start: 0.8015 (mp0) cc_final: 0.7794 (tt0) REVERT: B 354 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5351 (mt0) outliers start: 20 outliers final: 4 residues processed: 265 average time/residue: 0.1723 time to fit residues: 63.1851 Evaluate side-chains 167 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 354 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN E 96 GLN D 71 GLN D 96 GLN D 293 GLN A 19 GLN A 96 GLN A 293 GLN C 71 GLN C 96 GLN B 293 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.099541 restraints weight = 30885.798| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.23 r_work: 0.2858 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15930 Z= 0.165 Angle : 0.580 6.784 21625 Z= 0.308 Chirality : 0.039 0.155 2350 Planarity : 0.004 0.027 2730 Dihedral : 5.841 45.950 2150 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.30 % Allowed : 5.55 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1875 helix: 0.73 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.016 0.002 TYR D 236 PHE 0.021 0.002 PHE C 171 TRP 0.013 0.002 TRP A 93 HIS 0.003 0.001 HIS E 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (15930) covalent geometry : angle 0.58049 / 0.31 (21625) hydrogen bonds : bond 0.05466 / 3.66 ( 985) hydrogen bonds : angle 4.81086 / 3.53 ( 2815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.579 Fit side-chains REVERT: E 70 ASP cc_start: 0.7916 (t70) cc_final: 0.7560 (t0) REVERT: E 117 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7964 (mtp180) REVERT: E 168 ARG cc_start: 0.7811 (ttt-90) cc_final: 0.7491 (ttp-170) REVERT: D 159 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7604 (mp0) REVERT: D 168 ARG cc_start: 0.7825 (ttt-90) cc_final: 0.7313 (ttp-170) REVERT: D 198 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7897 (tt0) REVERT: A 13 ARG cc_start: 0.7200 (mtp-110) cc_final: 0.6994 (mtm110) REVERT: A 70 ASP cc_start: 0.8100 (t70) cc_final: 0.7805 (t0) REVERT: A 155 ASP cc_start: 0.8273 (m-30) cc_final: 0.7999 (m-30) REVERT: A 168 ARG cc_start: 0.7862 (ttt-90) cc_final: 0.7395 (ttp-170) REVERT: C 70 ASP cc_start: 0.8084 (t70) cc_final: 0.7716 (t0) REVERT: C 159 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7984 (mp0) REVERT: C 168 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.7206 (ttp-170) REVERT: C 197 ARG cc_start: 0.8438 (ttt90) cc_final: 0.8202 (tpt170) REVERT: B 70 ASP cc_start: 0.7816 (t70) cc_final: 0.7500 (t0) REVERT: B 168 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.7340 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 170 average time/residue: 0.1810 time to fit residues: 42.1872 Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain B residue 71 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN A 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100066 restraints weight = 31436.475| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.16 r_work: 0.2863 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15930 Z= 0.167 Angle : 0.540 6.029 21625 Z= 0.286 Chirality : 0.038 0.154 2350 Planarity : 0.003 0.026 2730 Dihedral : 4.863 45.772 2130 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.73 % Allowed : 5.55 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1875 helix: 0.84 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.37 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.015 0.002 TYR D 236 PHE 0.022 0.002 PHE B 309 TRP 0.013 0.002 TRP A 93 HIS 0.003 0.001 HIS E 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (15930) covalent geometry : angle 0.53994 / 0.29 (21625) hydrogen bonds : bond 0.05148 / 3.46 ( 985) hydrogen bonds : angle 4.67639 / 3.43 ( 2815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.615 Fit side-chains REVERT: E 70 ASP cc_start: 0.7881 (t70) cc_final: 0.7562 (t0) REVERT: E 117 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7997 (mtp180) REVERT: E 168 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7536 (ttp-170) REVERT: D 75 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7059 (pp) REVERT: D 159 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7611 (mp0) REVERT: D 168 ARG cc_start: 0.7923 (ttt-90) cc_final: 0.7428 (ttp-170) REVERT: D 198 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8020 (tt0) REVERT: D 319 MET cc_start: 0.8842 (mmt) cc_final: 0.8086 (mmt) REVERT: A 13 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.7095 (mtm110) REVERT: A 19 GLN cc_start: 0.8291 (mt0) cc_final: 0.8064 (mt0) REVERT: A 70 ASP cc_start: 0.8020 (t70) cc_final: 0.7758 (t0) REVERT: A 155 ASP cc_start: 0.8349 (m-30) cc_final: 0.8100 (m-30) REVERT: A 168 ARG cc_start: 0.7803 (ttt-90) cc_final: 0.7378 (ttp-170) REVERT: C 70 ASP cc_start: 0.8056 (t70) cc_final: 0.7712 (t0) REVERT: C 75 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7129 (pp) REVERT: C 159 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8087 (mp0) REVERT: C 168 ARG cc_start: 0.7908 (ttt-90) cc_final: 0.7216 (ttp-170) REVERT: B 70 ASP cc_start: 0.7856 (t70) cc_final: 0.7480 (t0) REVERT: B 168 ARG cc_start: 0.7785 (ttt-90) cc_final: 0.7413 (ttp-170) outliers start: 12 outliers final: 3 residues processed: 154 average time/residue: 0.1728 time to fit residues: 36.9226 Evaluate side-chains 145 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain A residue 601 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 8 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN A 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.129389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101666 restraints weight = 26528.107| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.95 r_work: 0.2898 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15930 Z= 0.158 Angle : 0.525 6.751 21625 Z= 0.277 Chirality : 0.037 0.154 2350 Planarity : 0.003 0.023 2730 Dihedral : 4.695 44.293 2130 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.55 % Allowed : 6.65 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1875 helix: 0.93 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 117 TYR 0.014 0.002 TYR E 236 PHE 0.019 0.002 PHE C 171 TRP 0.013 0.002 TRP C 93 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (15930) covalent geometry : angle 0.52473 / 0.28 (21625) hydrogen bonds : bond 0.04982 / 3.35 ( 985) hydrogen bonds : angle 4.60315 / 3.38 ( 2815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.614 Fit side-chains REVERT: E 70 ASP cc_start: 0.7853 (t70) cc_final: 0.7543 (t0) REVERT: E 117 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7922 (mtp180) REVERT: E 168 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7373 (ttp-170) REVERT: D 75 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7106 (pp) REVERT: D 159 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7594 (mp0) REVERT: D 168 ARG cc_start: 0.7892 (ttt-90) cc_final: 0.7427 (ttp-170) REVERT: D 198 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8021 (tt0) REVERT: D 319 MET cc_start: 0.8825 (mmt) cc_final: 0.7995 (mmt) REVERT: A 70 ASP cc_start: 0.7941 (t70) cc_final: 0.7703 (t0) REVERT: A 155 ASP cc_start: 0.8321 (m-30) cc_final: 0.8066 (m-30) REVERT: A 168 ARG cc_start: 0.7757 (ttt-90) cc_final: 0.7278 (ttp-170) REVERT: C 13 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7126 (mtm110) REVERT: C 70 ASP cc_start: 0.7972 (t70) cc_final: 0.7642 (t0) REVERT: C 75 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7023 (pp) REVERT: C 168 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7189 (ttp-170) REVERT: B 13 ARG cc_start: 0.7385 (mtm110) cc_final: 0.7038 (mtm110) REVERT: B 70 ASP cc_start: 0.7821 (t70) cc_final: 0.7453 (t0) REVERT: B 168 ARG cc_start: 0.7788 (ttt-90) cc_final: 0.7400 (ttp-170) outliers start: 9 outliers final: 2 residues processed: 150 average time/residue: 0.1787 time to fit residues: 36.9806 Evaluate side-chains 141 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 339 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 128 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN A 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.129073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098589 restraints weight = 39292.090| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.51 r_work: 0.2848 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15930 Z= 0.161 Angle : 0.524 7.428 21625 Z= 0.275 Chirality : 0.038 0.154 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.600 42.745 2130 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.37 % Allowed : 7.87 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1875 helix: 0.95 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.55 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.013 0.001 TYR E 236 PHE 0.018 0.002 PHE C 171 TRP 0.013 0.002 TRP C 93 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (15930) covalent geometry : angle 0.52442 / 0.28 (21625) hydrogen bonds : bond 0.04936 / 3.33 ( 985) hydrogen bonds : angle 4.55968 / 3.35 ( 2815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.514 Fit side-chains REVERT: E 70 ASP cc_start: 0.7709 (t70) cc_final: 0.7428 (t0) REVERT: E 117 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7787 (mtp180) REVERT: E 168 ARG cc_start: 0.7603 (ttt-90) cc_final: 0.7263 (ttp-170) REVERT: D 36 LEU cc_start: 0.8674 (tp) cc_final: 0.8444 (tp) REVERT: D 75 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7152 (pp) REVERT: D 168 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7315 (ttp-170) REVERT: D 198 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7918 (tt0) REVERT: A 70 ASP cc_start: 0.7819 (t70) cc_final: 0.7585 (t0) REVERT: A 155 ASP cc_start: 0.8217 (m-30) cc_final: 0.7960 (m-30) REVERT: A 168 ARG cc_start: 0.7675 (ttt-90) cc_final: 0.7249 (ttp-170) REVERT: C 13 ARG cc_start: 0.7409 (mtm110) cc_final: 0.7078 (mtm110) REVERT: C 70 ASP cc_start: 0.7872 (t70) cc_final: 0.7540 (t0) REVERT: C 75 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7004 (pp) REVERT: C 168 ARG cc_start: 0.7731 (ttt-90) cc_final: 0.7124 (ttp-170) REVERT: B 13 ARG cc_start: 0.7348 (mtm110) cc_final: 0.7003 (mtm110) REVERT: B 70 ASP cc_start: 0.7748 (t70) cc_final: 0.7411 (t0) REVERT: B 168 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.7283 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 150 average time/residue: 0.1824 time to fit residues: 37.3583 Evaluate side-chains 143 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain E residue 601 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN B 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100148 restraints weight = 38752.954| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.37 r_work: 0.2862 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15930 Z= 0.141 Angle : 0.502 7.000 21625 Z= 0.264 Chirality : 0.037 0.154 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.488 42.519 2130 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.43 % Allowed : 8.54 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1875 helix: 1.05 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.011 0.001 TYR D 97 PHE 0.017 0.001 PHE C 171 TRP 0.013 0.001 TRP C 93 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15930) covalent geometry : angle 0.50220 / 0.26 (21625) hydrogen bonds : bond 0.04784 / 3.22 ( 985) hydrogen bonds : angle 4.49742 / 3.31 ( 2815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7697 (t70) cc_final: 0.7428 (t0) REVERT: E 168 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.7247 (ttp-170) REVERT: D 36 LEU cc_start: 0.8675 (tp) cc_final: 0.8420 (tp) REVERT: D 75 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7140 (pp) REVERT: D 168 ARG cc_start: 0.7790 (ttt-90) cc_final: 0.7336 (ttp-170) REVERT: D 198 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7918 (tt0) REVERT: A 70 ASP cc_start: 0.7819 (t70) cc_final: 0.7576 (t0) REVERT: A 155 ASP cc_start: 0.8241 (m-30) cc_final: 0.7992 (m-30) REVERT: A 168 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7241 (ttp-170) REVERT: C 13 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7139 (mtm110) REVERT: C 14 PHE cc_start: 0.8579 (t80) cc_final: 0.8268 (t80) REVERT: C 70 ASP cc_start: 0.7774 (t70) cc_final: 0.7456 (t0) REVERT: C 75 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7047 (pp) REVERT: C 168 ARG cc_start: 0.7777 (ttt-90) cc_final: 0.7185 (ttp-170) REVERT: B 13 ARG cc_start: 0.7379 (mtm110) cc_final: 0.7053 (mtm110) REVERT: B 70 ASP cc_start: 0.7737 (t70) cc_final: 0.7407 (t0) REVERT: B 168 ARG cc_start: 0.7625 (ttt-90) cc_final: 0.7275 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 145 average time/residue: 0.1749 time to fit residues: 34.9174 Evaluate side-chains 140 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain E residue 601 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 133 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.097585 restraints weight = 39856.283| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.62 r_work: 0.2840 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15930 Z= 0.159 Angle : 0.512 6.628 21625 Z= 0.270 Chirality : 0.037 0.153 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.508 43.912 2130 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.55 % Allowed : 8.60 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1875 helix: 1.05 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.012 0.001 TYR E 236 PHE 0.018 0.002 PHE C 171 TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15930) covalent geometry : angle 0.51213 / 0.27 (21625) hydrogen bonds : bond 0.04868 / 3.29 ( 985) hydrogen bonds : angle 4.50584 / 3.31 ( 2815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7705 (t70) cc_final: 0.7409 (t0) REVERT: E 168 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.7193 (ttp-170) REVERT: D 75 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7090 (pp) REVERT: D 168 ARG cc_start: 0.7780 (ttt-90) cc_final: 0.7269 (ttp-170) REVERT: D 198 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7941 (tt0) REVERT: A 70 ASP cc_start: 0.7798 (t70) cc_final: 0.7557 (t0) REVERT: A 155 ASP cc_start: 0.8258 (m-30) cc_final: 0.7987 (m-30) REVERT: A 168 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7194 (ttp-170) REVERT: C 13 ARG cc_start: 0.7441 (mtm110) cc_final: 0.7140 (mtm110) REVERT: C 70 ASP cc_start: 0.7795 (t70) cc_final: 0.7472 (t0) REVERT: C 75 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7042 (pp) REVERT: C 168 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7116 (ttp-170) REVERT: B 13 ARG cc_start: 0.7363 (mtm110) cc_final: 0.7013 (mtm110) REVERT: B 70 ASP cc_start: 0.7733 (t70) cc_final: 0.7362 (t0) REVERT: B 168 ARG cc_start: 0.7619 (ttt-90) cc_final: 0.7214 (ttp-170) REVERT: E 601 GLU cc_start: 0.5330 (OUTLIER) cc_final: 0.5128 (tp30) outliers start: 9 outliers final: 3 residues processed: 141 average time/residue: 0.1666 time to fit residues: 32.3953 Evaluate side-chains 138 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain E residue 601 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 150 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.129885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098852 restraints weight = 40372.462| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.61 r_work: 0.2853 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15930 Z= 0.142 Angle : 0.497 6.290 21625 Z= 0.262 Chirality : 0.037 0.153 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.446 43.627 2130 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.37 % Allowed : 8.72 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1875 helix: 1.10 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.67 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.011 0.001 TYR D 337 PHE 0.017 0.001 PHE C 171 TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15930) covalent geometry : angle 0.49669 / 0.26 (21625) hydrogen bonds : bond 0.04768 / 3.21 ( 985) hydrogen bonds : angle 4.46932 / 3.28 ( 2815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7664 (t70) cc_final: 0.7379 (t0) REVERT: E 168 ARG cc_start: 0.7572 (ttt-90) cc_final: 0.7178 (ttp-170) REVERT: D 36 LEU cc_start: 0.8593 (tp) cc_final: 0.8388 (tp) REVERT: D 75 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7086 (pp) REVERT: D 168 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7258 (ttp-170) REVERT: D 198 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7934 (tt0) REVERT: D 364 THR cc_start: 0.8899 (p) cc_final: 0.8673 (t) REVERT: A 70 ASP cc_start: 0.7781 (t70) cc_final: 0.7547 (t0) REVERT: A 155 ASP cc_start: 0.8246 (m-30) cc_final: 0.7976 (m-30) REVERT: A 168 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7204 (ttp-170) REVERT: C 13 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7126 (mtm110) REVERT: C 14 PHE cc_start: 0.8545 (t80) cc_final: 0.8231 (t80) REVERT: C 70 ASP cc_start: 0.7808 (t70) cc_final: 0.7490 (t0) REVERT: C 75 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7103 (pp) REVERT: C 168 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7106 (ttp-170) REVERT: B 13 ARG cc_start: 0.7378 (mtm110) cc_final: 0.7033 (mtm110) REVERT: B 70 ASP cc_start: 0.7733 (t70) cc_final: 0.7368 (t0) REVERT: B 168 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7204 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 144 average time/residue: 0.1685 time to fit residues: 33.4085 Evaluate side-chains 142 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain B residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 148 optimal weight: 0.0010 chunk 175 optimal weight: 0.0980 chunk 108 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100836 restraints weight = 40705.699| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.57 r_work: 0.2867 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15930 Z= 0.129 Angle : 0.491 8.148 21625 Z= 0.259 Chirality : 0.037 0.154 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.374 43.583 2130 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.49 % Allowed : 8.66 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1875 helix: 1.16 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.68 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.010 0.001 TYR B 97 PHE 0.016 0.001 PHE C 171 TRP 0.013 0.001 TRP B 93 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15930) covalent geometry : angle 0.49069 / 0.26 (21625) hydrogen bonds : bond 0.04668 / 3.14 ( 985) hydrogen bonds : angle 4.40516 / 3.24 ( 2815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7645 (t70) cc_final: 0.7387 (t0) REVERT: E 168 ARG cc_start: 0.7567 (ttt-90) cc_final: 0.7209 (ttp-170) REVERT: D 36 LEU cc_start: 0.8610 (tp) cc_final: 0.8398 (tp) REVERT: D 75 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7093 (pp) REVERT: D 168 ARG cc_start: 0.7778 (ttt-90) cc_final: 0.7284 (ttp-170) REVERT: D 198 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7929 (tt0) REVERT: D 223 MET cc_start: 0.8581 (mmm) cc_final: 0.8220 (mmp) REVERT: D 364 THR cc_start: 0.8917 (p) cc_final: 0.8682 (t) REVERT: A 155 ASP cc_start: 0.8261 (m-30) cc_final: 0.8015 (m-30) REVERT: A 168 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.7239 (ttp-170) REVERT: C 13 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7183 (mtm110) REVERT: C 14 PHE cc_start: 0.8540 (t80) cc_final: 0.8239 (t80) REVERT: C 70 ASP cc_start: 0.7796 (t70) cc_final: 0.7475 (t0) REVERT: C 75 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7109 (pp) REVERT: C 168 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.7140 (ttp-170) REVERT: B 13 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7068 (mtm110) REVERT: B 70 ASP cc_start: 0.7719 (t70) cc_final: 0.7370 (t0) REVERT: B 168 ARG cc_start: 0.7618 (ttt-90) cc_final: 0.7241 (ttp-170) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 0.1613 time to fit residues: 31.9672 Evaluate side-chains 140 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 71 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 61 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099669 restraints weight = 36970.325| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.38 r_work: 0.2858 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15930 Z= 0.156 Angle : 0.511 6.946 21625 Z= 0.269 Chirality : 0.038 0.192 2350 Planarity : 0.003 0.025 2730 Dihedral : 4.411 44.247 2130 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.49 % Allowed : 9.15 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1875 helix: 1.10 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.70 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 117 TYR 0.011 0.001 TYR D 236 PHE 0.018 0.002 PHE C 171 TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (15930) covalent geometry : angle 0.51104 / 0.27 (21625) hydrogen bonds : bond 0.04803 / 3.24 ( 985) hydrogen bonds : angle 4.46053 / 3.28 ( 2815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.424 Fit side-chains REVERT: E 70 ASP cc_start: 0.7646 (t70) cc_final: 0.7374 (t0) REVERT: E 168 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.7175 (ttp-170) REVERT: D 36 LEU cc_start: 0.8592 (tp) cc_final: 0.8375 (tp) REVERT: D 75 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7087 (pp) REVERT: D 168 ARG cc_start: 0.7778 (ttt-90) cc_final: 0.7272 (ttp-170) REVERT: D 198 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7918 (tt0) REVERT: D 223 MET cc_start: 0.8578 (mmm) cc_final: 0.8177 (mmp) REVERT: D 364 THR cc_start: 0.8917 (p) cc_final: 0.8707 (t) REVERT: A 155 ASP cc_start: 0.8235 (m-30) cc_final: 0.7981 (m-30) REVERT: A 168 ARG cc_start: 0.7668 (ttt-90) cc_final: 0.7201 (ttp-170) REVERT: C 13 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7150 (mtm110) REVERT: C 14 PHE cc_start: 0.8545 (t80) cc_final: 0.8223 (t80) REVERT: C 70 ASP cc_start: 0.7805 (t70) cc_final: 0.7477 (t0) REVERT: C 75 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7114 (pp) REVERT: C 168 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7118 (ttp-170) REVERT: B 70 ASP cc_start: 0.7770 (t70) cc_final: 0.7383 (t0) REVERT: B 168 ARG cc_start: 0.7595 (ttt-90) cc_final: 0.7203 (ttp-170) outliers start: 8 outliers final: 4 residues processed: 134 average time/residue: 0.1473 time to fit residues: 26.9065 Evaluate side-chains 139 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 71 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 167 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 123 optimal weight: 0.0670 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 0.0270 chunk 71 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 GLN D 71 GLN A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103090 restraints weight = 40469.680| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.42 r_work: 0.2906 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 15930 Z= 0.115 Angle : 0.477 7.023 21625 Z= 0.251 Chirality : 0.036 0.166 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.246 43.385 2130 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.24 % Allowed : 9.33 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1875 helix: 1.17 (0.14), residues: 1325 sheet: None (None), residues: 0 loop : -0.85 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.009 0.001 TYR C 97 PHE 0.015 0.001 PHE A 171 TRP 0.013 0.001 TRP B 93 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15930) covalent geometry : angle 0.47745 / 0.25 (21625) hydrogen bonds : bond 0.04496 / 3.02 ( 985) hydrogen bonds : angle 4.34492 / 3.19 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.43 seconds wall clock time: 65 minutes 27.77 seconds (3927.77 seconds total)