Starting phenix.real_space_refine on Thu Feb 5 05:33:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyi_47305/02_2026/9dyi_47305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyi_47305/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dyi_47305/02_2026/9dyi_47305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyi_47305/02_2026/9dyi_47305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyi_47305/02_2026/9dyi_47305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyi_47305/02_2026/9dyi_47305.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.32 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: 1.20 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: 0.44 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: 2.66 Time building geometry restraints manager: 1.56 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.590 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 covalent geometry : bond 0.01435 (15930) covalent geometry : angle 1.70974 (21625) hydrogen bonds : bond 0.14675 ( 985) hydrogen bonds : angle 6.20100 ( 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 : 0.556 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: 0.6376 (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: 0.5682 (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: 0.1671 time to fit residues: 60.6751 Evaluate side-chains 170 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.099300 restraints weight = 30704.048| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.24 r_work: 0.2858 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 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 = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15930 Z= 0.165 Angle : 0.576 6.875 21625 Z= 0.306 Chirality : 0.039 0.154 2350 Planarity : 0.004 0.026 2730 Dihedral : 5.772 45.059 2150 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.51 % 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 (0.19), residues: 1875 helix: 0.71 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.32 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 255 TYR 0.017 0.002 TYR D 236 PHE 0.022 0.002 PHE E 171 TRP 0.013 0.002 TRP A 93 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00362 (15930) covalent geometry : angle 0.57607 (21625) hydrogen bonds : bond 0.05415 ( 985) hydrogen bonds : angle 4.78062 ( 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 174 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.533 Fit side-chains REVERT: E 70 ASP cc_start: 0.7912 (t70) cc_final: 0.7550 (t0) REVERT: E 117 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7993 (mtp180) REVERT: E 168 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7478 (ttp-170) REVERT: D 159 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7634 (mp0) REVERT: D 168 ARG cc_start: 0.7852 (ttt-90) cc_final: 0.7339 (ttp-170) REVERT: D 198 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7898 (tt0) REVERT: A 13 ARG cc_start: 0.7151 (mtp-110) cc_final: 0.6923 (mtm110) REVERT: A 70 ASP cc_start: 0.8078 (t70) cc_final: 0.7786 (t0) REVERT: A 155 ASP cc_start: 0.8266 (m-30) cc_final: 0.7985 (m-30) REVERT: A 168 ARG cc_start: 0.7805 (ttt-90) cc_final: 0.7333 (ttp-170) REVERT: C 70 ASP cc_start: 0.8072 (t70) cc_final: 0.7701 (t0) REVERT: C 159 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7993 (mp0) REVERT: C 168 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7184 (ttp-170) REVERT: C 197 ARG cc_start: 0.8444 (ttt90) cc_final: 0.8203 (tpt170) REVERT: B 70 ASP cc_start: 0.7820 (t70) cc_final: 0.7498 (t0) REVERT: B 168 ARG cc_start: 0.7757 (ttt-90) cc_final: 0.7354 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 171 average time/residue: 0.1648 time to fit residues: 38.4561 Evaluate side-chains 147 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 0.6980 chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3381 r_free = 0.3381 target = 0.129739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.100858 restraints weight = 31770.939| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.15 r_work: 0.2880 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15930 Z= 0.150 Angle : 0.528 6.710 21625 Z= 0.279 Chirality : 0.037 0.155 2350 Planarity : 0.003 0.025 2730 Dihedral : 4.812 44.426 2130 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.91 % Allowed : 5.06 % Favored : 94.02 % 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: 0.65 (0.19), residues: 1875 helix: 0.87 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.38 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 255 TYR 0.013 0.002 TYR D 236 PHE 0.023 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 covalent geometry : bond 0.00330 (15930) covalent geometry : angle 0.52787 (21625) hydrogen bonds : bond 0.05040 ( 985) hydrogen bonds : angle 4.62444 ( 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 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.657 Fit side-chains REVERT: E 70 ASP cc_start: 0.7848 (t70) cc_final: 0.7529 (t0) REVERT: E 117 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7985 (mtp180) REVERT: E 168 ARG cc_start: 0.7845 (ttt-90) cc_final: 0.7522 (ttp-170) REVERT: D 75 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7032 (pp) REVERT: D 159 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7667 (mp0) REVERT: D 168 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7425 (ttp-170) REVERT: D 198 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7944 (tt0) REVERT: D 223 MET cc_start: 0.8741 (mmm) cc_final: 0.8540 (mmp) REVERT: A 13 ARG cc_start: 0.7304 (mtp-110) cc_final: 0.7015 (mtm110) REVERT: A 19 GLN cc_start: 0.8267 (mt0) cc_final: 0.8024 (mt0) REVERT: A 70 ASP cc_start: 0.7993 (t70) cc_final: 0.7733 (t0) REVERT: A 155 ASP cc_start: 0.8354 (m-30) cc_final: 0.8098 (m-30) REVERT: A 168 ARG cc_start: 0.7773 (ttt-90) cc_final: 0.7360 (ttp-170) REVERT: C 70 ASP cc_start: 0.8020 (t70) cc_final: 0.7695 (t0) REVERT: C 75 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7133 (pp) REVERT: C 168 ARG cc_start: 0.7880 (ttt-90) cc_final: 0.7195 (ttp-170) REVERT: B 70 ASP cc_start: 0.7826 (t70) cc_final: 0.7453 (t0) REVERT: B 75 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7022 (pp) REVERT: B 168 ARG cc_start: 0.7778 (ttt-90) cc_final: 0.7428 (ttp-170) outliers start: 15 outliers final: 4 residues processed: 161 average time/residue: 0.1881 time to fit residues: 41.5850 Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LYS 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 B residue 75 LEU 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: 0.5980 chunk 132 optimal weight: 2.9990 chunk 64 optimal weight: 0.0050 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN A 71 GLN A 115 HIS B 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.130636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102864 restraints weight = 26318.755| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.96 r_work: 0.2927 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15930 Z= 0.137 Angle : 0.508 5.823 21625 Z= 0.268 Chirality : 0.037 0.155 2350 Planarity : 0.003 0.023 2730 Dihedral : 4.615 44.023 2130 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.37 % Allowed : 6.52 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1875 helix: 0.99 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 117 TYR 0.011 0.001 TYR E 236 PHE 0.018 0.002 PHE B 171 TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00296 (15930) covalent geometry : angle 0.50837 (21625) hydrogen bonds : bond 0.04831 ( 985) hydrogen bonds : angle 4.52868 ( 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 150 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.649 Fit side-chains REVERT: E 70 ASP cc_start: 0.7844 (t70) cc_final: 0.7548 (t0) REVERT: E 117 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7897 (mtp180) REVERT: E 168 ARG cc_start: 0.7778 (ttt-90) cc_final: 0.7433 (ttp-170) REVERT: D 75 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7090 (pp) REVERT: D 159 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7623 (mp0) REVERT: D 168 ARG cc_start: 0.7877 (ttt-90) cc_final: 0.7408 (ttp-170) REVERT: D 198 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8022 (tt0) REVERT: A 70 ASP cc_start: 0.7914 (t70) cc_final: 0.7679 (t0) REVERT: A 155 ASP cc_start: 0.8341 (m-30) cc_final: 0.8082 (m-30) REVERT: A 168 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7268 (ttp-170) REVERT: C 13 ARG cc_start: 0.7411 (mtm110) cc_final: 0.7079 (mtm110) REVERT: C 70 ASP cc_start: 0.7942 (t70) cc_final: 0.7622 (t0) REVERT: C 75 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7098 (pp) REVERT: C 168 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7183 (ttp-170) REVERT: B 13 ARG cc_start: 0.7343 (mtm110) cc_final: 0.7017 (mtm110) REVERT: B 70 ASP cc_start: 0.7792 (t70) cc_final: 0.7457 (t0) REVERT: B 168 ARG cc_start: 0.7783 (ttt-90) cc_final: 0.7397 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 145 average time/residue: 0.1912 time to fit residues: 38.0007 Evaluate side-chains 140 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 143 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3368 r_free = 0.3368 target = 0.128598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.098042 restraints weight = 39100.059| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.46 r_work: 0.2823 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2065 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= 0.171 Angle : 0.528 6.690 21625 Z= 0.277 Chirality : 0.038 0.209 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.607 43.285 2130 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.43 % Allowed : 7.74 % Favored : 91.83 % 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: 0.69 (0.19), residues: 1875 helix: 0.96 (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 B 255 TYR 0.015 0.002 TYR E 236 PHE 0.019 0.002 PHE B 171 TRP 0.013 0.002 TRP A 93 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00388 (15930) covalent geometry : angle 0.52833 (21625) hydrogen bonds : bond 0.04970 ( 985) hydrogen bonds : angle 4.55572 ( 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 151 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.639 Fit side-chains REVERT: E 70 ASP cc_start: 0.7732 (t70) cc_final: 0.7430 (t0) REVERT: E 117 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7802 (mtp180) REVERT: E 168 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7226 (ttp-170) REVERT: D 75 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7127 (pp) REVERT: D 159 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7443 (mp0) REVERT: D 168 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7316 (ttp-170) REVERT: D 198 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7899 (tt0) REVERT: A 70 ASP cc_start: 0.7824 (t70) cc_final: 0.7585 (t0) REVERT: A 155 ASP cc_start: 0.8221 (m-30) cc_final: 0.7956 (m-30) REVERT: A 168 ARG cc_start: 0.7646 (ttt-90) cc_final: 0.7213 (ttp-170) REVERT: C 13 ARG cc_start: 0.7373 (mtm110) cc_final: 0.7064 (mtm110) REVERT: C 70 ASP cc_start: 0.7880 (t70) cc_final: 0.7549 (t0) REVERT: C 75 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7008 (pp) REVERT: C 168 ARG cc_start: 0.7731 (ttt-90) cc_final: 0.7100 (ttp-170) REVERT: B 13 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6954 (mtm110) REVERT: B 70 ASP cc_start: 0.7732 (t70) cc_final: 0.7375 (t0) REVERT: B 168 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7270 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 145 average time/residue: 0.1901 time to fit residues: 37.7031 Evaluate side-chains 146 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LYS 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 601 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 168 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3414 r_free = 0.3414 target = 0.131863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101717 restraints weight = 38285.253| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.45 r_work: 0.2863 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15930 Z= 0.134 Angle : 0.495 6.380 21625 Z= 0.260 Chirality : 0.036 0.154 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.464 42.016 2130 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.55 % Allowed : 8.29 % Favored : 91.16 % 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: 0.80 (0.19), residues: 1875 helix: 1.10 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.69 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.010 0.001 TYR D 97 PHE 0.017 0.001 PHE C 171 TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00291 (15930) covalent geometry : angle 0.49458 (21625) hydrogen bonds : bond 0.04722 ( 985) hydrogen bonds : angle 4.46158 ( 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 160 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7658 (t70) cc_final: 0.7394 (t0) REVERT: E 168 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7229 (ttp-170) REVERT: D 75 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7104 (pp) REVERT: D 168 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7336 (ttp-170) REVERT: D 198 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7934 (tt0) REVERT: A 70 ASP cc_start: 0.7782 (t70) cc_final: 0.7553 (t0) REVERT: A 155 ASP cc_start: 0.8227 (m-30) cc_final: 0.7976 (m-30) REVERT: A 168 ARG cc_start: 0.7616 (ttt-90) cc_final: 0.7217 (ttp-170) REVERT: C 13 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7113 (mtm110) REVERT: C 14 PHE cc_start: 0.8598 (t80) cc_final: 0.8318 (t80) REVERT: C 70 ASP cc_start: 0.7775 (t70) cc_final: 0.7466 (t0) REVERT: C 75 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7010 (pp) REVERT: C 168 ARG cc_start: 0.7789 (ttt-90) cc_final: 0.7192 (ttp-170) REVERT: B 13 ARG cc_start: 0.7349 (mtm110) cc_final: 0.7036 (mtm110) REVERT: B 70 ASP cc_start: 0.7726 (t70) cc_final: 0.7405 (t0) REVERT: B 168 ARG cc_start: 0.7663 (ttt-90) cc_final: 0.7307 (ttp-170) outliers start: 9 outliers final: 3 residues processed: 152 average time/residue: 0.1763 time to fit residues: 36.9415 Evaluate side-chains 146 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 153 THR 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: 1.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3389 r_free = 0.3389 target = 0.130057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.099679 restraints weight = 39564.466| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.47 r_work: 0.2852 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15930 Z= 0.150 Angle : 0.509 6.456 21625 Z= 0.267 Chirality : 0.037 0.154 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.469 42.701 2130 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.67 % Allowed : 8.66 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1875 helix: 1.09 (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 0.012 0.001 TYR E 236 PHE 0.017 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 covalent geometry : bond 0.00333 (15930) covalent geometry : angle 0.50901 (21625) hydrogen bonds : bond 0.04803 ( 985) hydrogen bonds : angle 4.47466 ( 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 155 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7692 (t70) cc_final: 0.7422 (t0) REVERT: E 168 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7237 (ttp-170) REVERT: D 75 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7108 (pp) REVERT: D 168 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7326 (ttp-170) REVERT: D 198 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7940 (tt0) REVERT: A 70 ASP cc_start: 0.7784 (t70) cc_final: 0.7553 (t0) REVERT: A 155 ASP cc_start: 0.8261 (m-30) cc_final: 0.8001 (m-30) REVERT: A 168 ARG cc_start: 0.7655 (ttt-90) cc_final: 0.7232 (ttp-170) REVERT: C 13 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7106 (mtm110) REVERT: C 14 PHE cc_start: 0.8602 (t80) cc_final: 0.8321 (t80) REVERT: C 70 ASP cc_start: 0.7779 (t70) cc_final: 0.7456 (t0) REVERT: C 75 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7038 (pp) REVERT: C 168 ARG cc_start: 0.7771 (ttt-90) cc_final: 0.7166 (ttp-170) REVERT: B 13 ARG cc_start: 0.7365 (mtm110) cc_final: 0.7039 (mtm110) REVERT: B 70 ASP cc_start: 0.7736 (t70) cc_final: 0.7378 (t0) REVERT: B 168 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.7299 (ttp-170) outliers start: 11 outliers final: 5 residues processed: 146 average time/residue: 0.1797 time to fit residues: 35.9737 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 : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain D residue 30 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 0.0050 chunk 150 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3402 r_free = 0.3402 target = 0.131641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101062 restraints weight = 39789.737| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.58 r_work: 0.2882 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15930 Z= 0.121 Angle : 0.481 5.530 21625 Z= 0.253 Chirality : 0.036 0.162 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.358 42.081 2130 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.49 % Allowed : 8.84 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1875 helix: 1.20 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.72 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.010 0.001 TYR D 97 PHE 0.017 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 covalent geometry : bond 0.00254 (15930) covalent geometry : angle 0.48141 (21625) hydrogen bonds : bond 0.04591 ( 985) hydrogen bonds : angle 4.39153 ( 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 155 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7665 (t70) cc_final: 0.7398 (t0) REVERT: E 168 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.7188 (ttp-170) REVERT: D 75 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7065 (pp) REVERT: D 168 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.7280 (ttp-170) REVERT: D 198 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7959 (tt0) REVERT: A 13 ARG cc_start: 0.7379 (mtm110) cc_final: 0.7042 (mtm180) REVERT: A 70 ASP cc_start: 0.7729 (t70) cc_final: 0.7511 (t0) REVERT: A 155 ASP cc_start: 0.8259 (m-30) cc_final: 0.8017 (m-30) REVERT: A 168 ARG cc_start: 0.7616 (ttt-90) cc_final: 0.7203 (ttp-170) REVERT: C 13 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7125 (mtm110) REVERT: C 14 PHE cc_start: 0.8570 (t80) cc_final: 0.8321 (t80) REVERT: C 70 ASP cc_start: 0.7769 (t70) cc_final: 0.7467 (t0) REVERT: C 75 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7012 (pp) REVERT: C 168 ARG cc_start: 0.7765 (ttt-90) cc_final: 0.7129 (ttp-170) REVERT: B 13 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7029 (mtm110) REVERT: B 70 ASP cc_start: 0.7684 (t70) cc_final: 0.7338 (t0) REVERT: B 168 ARG cc_start: 0.7616 (ttt-90) cc_final: 0.7223 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 149 average time/residue: 0.1688 time to fit residues: 34.7710 Evaluate side-chains 147 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain D residue 30 LYS 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 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 chunk 175 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101386 restraints weight = 40597.041| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.60 r_work: 0.2871 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15930 Z= 0.126 Angle : 0.485 8.325 21625 Z= 0.255 Chirality : 0.036 0.181 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.291 42.322 2130 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.55 % Allowed : 9.02 % 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: 0.81 (0.19), residues: 1875 helix: 1.13 (0.14), residues: 1325 sheet: None (None), residues: 0 loop : -0.82 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.011 0.001 TYR D 97 PHE 0.020 0.001 PHE A 14 TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00266 (15930) covalent geometry : angle 0.48539 (21625) hydrogen bonds : bond 0.04589 ( 985) hydrogen bonds : angle 4.38288 ( 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 155 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.7635 (t70) cc_final: 0.7377 (t0) REVERT: E 168 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.7201 (ttp-170) REVERT: D 13 ARG cc_start: 0.7295 (mtm110) cc_final: 0.7090 (mtm110) REVERT: D 75 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7042 (pp) REVERT: D 168 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.7317 (ttp-170) REVERT: A 13 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7041 (mtm180) REVERT: A 155 ASP cc_start: 0.8240 (m-30) cc_final: 0.8001 (m-30) REVERT: A 168 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7232 (ttp-170) REVERT: C 13 ARG cc_start: 0.7387 (mtm110) cc_final: 0.7144 (mtm110) REVERT: C 14 PHE cc_start: 0.8580 (t80) cc_final: 0.8334 (t80) REVERT: C 70 ASP cc_start: 0.7744 (t70) cc_final: 0.7453 (t0) REVERT: C 75 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7021 (pp) REVERT: C 165 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7709 (mmt180) REVERT: C 168 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7127 (ttp-170) REVERT: B 13 ARG cc_start: 0.7385 (mtm110) cc_final: 0.7075 (mtm110) REVERT: B 70 ASP cc_start: 0.7676 (t70) cc_final: 0.7324 (t0) REVERT: B 168 ARG cc_start: 0.7580 (ttt-90) cc_final: 0.7228 (ttp-170) outliers start: 9 outliers final: 6 residues processed: 147 average time/residue: 0.1776 time to fit residues: 35.9559 Evaluate side-chains 147 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain D residue 30 LYS 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 71 GLN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 61 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101575 restraints weight = 36373.026| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.30 r_work: 0.2882 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15930 Z= 0.133 Angle : 0.489 6.829 21625 Z= 0.257 Chirality : 0.037 0.161 2350 Planarity : 0.003 0.026 2730 Dihedral : 4.308 42.867 2130 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.49 % Allowed : 9.09 % 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: 0.80 (0.19), residues: 1875 helix: 1.13 (0.14), residues: 1325 sheet: None (None), residues: 0 loop : -0.84 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.010 0.001 TYR D 97 PHE 0.020 0.001 PHE A 14 TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00287 (15930) covalent geometry : angle 0.48949 (21625) hydrogen bonds : bond 0.04628 ( 985) hydrogen bonds : angle 4.39593 ( 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 151 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.609 Fit side-chains REVERT: E 70 ASP cc_start: 0.7598 (t70) cc_final: 0.7331 (t0) REVERT: E 168 ARG cc_start: 0.7562 (ttt-90) cc_final: 0.7172 (ttp-170) REVERT: D 13 ARG cc_start: 0.7276 (mtm110) cc_final: 0.7063 (mtm110) REVERT: D 75 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7079 (pp) REVERT: D 168 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7297 (ttp-170) REVERT: A 13 ARG cc_start: 0.7312 (mtm110) cc_final: 0.6985 (mtm180) REVERT: A 155 ASP cc_start: 0.8243 (m-30) cc_final: 0.8000 (m-30) REVERT: A 168 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7233 (ttp-170) REVERT: C 13 ARG cc_start: 0.7348 (mtm110) cc_final: 0.7106 (mtm110) REVERT: C 14 PHE cc_start: 0.8565 (t80) cc_final: 0.8321 (t80) REVERT: C 70 ASP cc_start: 0.7715 (t70) cc_final: 0.7432 (t0) REVERT: C 75 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7005 (pp) REVERT: C 165 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7707 (mmt180) REVERT: C 168 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7105 (ttp-170) REVERT: B 70 ASP cc_start: 0.7665 (t70) cc_final: 0.7311 (t0) REVERT: B 168 ARG cc_start: 0.7571 (ttt-90) cc_final: 0.7201 (ttp-170) outliers start: 8 outliers final: 6 residues processed: 144 average time/residue: 0.1781 time to fit residues: 35.1747 Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain D residue 30 LYS 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 71 GLN Chi-restraints excluded: chain B residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 167 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 71 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.131695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101432 restraints weight = 41088.096| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.52 r_work: 0.2872 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 15930 Z= 0.131 Angle : 0.491 7.020 21625 Z= 0.258 Chirality : 0.037 0.154 2350 Planarity : 0.003 0.024 2730 Dihedral : 4.297 42.968 2130 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.55 % Allowed : 9.33 % Favored : 90.12 % 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: 0.77 (0.19), residues: 1875 helix: 1.12 (0.14), residues: 1330 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.010 0.001 TYR D 97 PHE 0.019 0.001 PHE A 14 TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00282 (15930) covalent geometry : angle 0.49134 (21625) hydrogen bonds : bond 0.04622 ( 985) hydrogen bonds : angle 4.38903 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3813.92 seconds wall clock time: 66 minutes 23.56 seconds (3983.56 seconds total)