Starting phenix.real_space_refine on Sat Aug 23 23:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyl_47308/08_2025/9dyl_47308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyl_47308/08_2025/9dyl_47308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dyl_47308/08_2025/9dyl_47308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyl_47308/08_2025/9dyl_47308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyl_47308/08_2025/9dyl_47308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyl_47308/08_2025/9dyl_47308.map" } resolution = 2.6 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= 0.003 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 C 10295 2.51 5 N 2555 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15645 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.79, per 1000 atoms: 0.18 Number of scatterers: 15645 At special positions: 0 Unit cell: (105.41, 107.07, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 80 16.00 O 2710 8.00 N 2555 7.00 C 10295 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: 1.04 Conformation dependent library (CDL) restraints added in 452.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 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: 92 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.902A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.597A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 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 175 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.001A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.603A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (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 369 through 374 removed outlier: 3.618A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.913A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 3.601A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 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 175 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 4.008A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.589A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (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 369 through 374 removed outlier: 3.615A pdb=" N GLU E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.906A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.594A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 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 175 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 4.008A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.591A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (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 369 through 374 removed outlier: 3.615A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.902A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.596A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 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 175 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.712A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 4.002A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.591A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (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 369 through 374 removed outlier: 3.618A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.907A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 3.600A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 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 175 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.003A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.594A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (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 369 through 374 removed outlier: 3.618A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3912 1.32 - 1.46: 3399 1.46 - 1.59: 8669 1.59 - 1.72: 0 1.72 - 1.85: 135 Bond restraints: 16115 Sorted by residual: bond pdb=" C ARG C 105 " pdb=" O ARG C 105 " ideal model delta sigma weight residual 1.236 1.289 -0.052 1.15e-02 7.56e+03 2.08e+01 bond pdb=" C VAL B 110 " pdb=" O VAL B 110 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.12e-02 7.97e+03 2.00e+01 bond pdb=" C ARG D 105 " pdb=" O ARG D 105 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.79e+01 bond pdb=" C VAL E 110 " pdb=" O VAL E 110 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.12e-02 7.97e+03 1.77e+01 bond pdb=" C VAL D 110 " pdb=" O VAL D 110 " ideal model delta sigma weight residual 1.237 1.283 -0.047 1.12e-02 7.97e+03 1.74e+01 ... (remaining 16110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 16186 1.37 - 2.74: 5080 2.74 - 4.11: 620 4.11 - 5.48: 50 5.48 - 6.85: 14 Bond angle restraints: 21950 Sorted by residual: angle pdb=" N THR C 91 " pdb=" CA THR C 91 " pdb=" C THR C 91 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.20e+01 angle pdb=" CA GLU A 300 " pdb=" C GLU A 300 " pdb=" O GLU A 300 " ideal model delta sigma weight residual 119.95 115.52 4.43 1.21e+00 6.83e-01 1.34e+01 angle pdb=" CA GLU D 300 " pdb=" C GLU D 300 " pdb=" O GLU D 300 " ideal model delta sigma weight residual 119.95 115.73 4.22 1.21e+00 6.83e-01 1.21e+01 angle pdb=" N ILE A 232 " pdb=" CA ILE A 232 " pdb=" C ILE A 232 " ideal model delta sigma weight residual 108.96 105.13 3.83 1.10e+00 8.26e-01 1.21e+01 angle pdb=" N PHE C 281 " pdb=" CA PHE C 281 " pdb=" C PHE C 281 " ideal model delta sigma weight residual 110.97 107.18 3.79 1.09e+00 8.42e-01 1.21e+01 ... (remaining 21945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8499 17.87 - 35.73: 732 35.73 - 53.60: 89 53.60 - 71.46: 25 71.46 - 89.33: 35 Dihedral angle restraints: 9380 sinusoidal: 3815 harmonic: 5565 Sorted by residual: dihedral pdb=" CA LEU C 32 " pdb=" C LEU C 32 " pdb=" N TYR C 33 " pdb=" CA TYR C 33 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N TYR B 33 " pdb=" CA TYR B 33 " ideal model delta harmonic sigma weight residual 180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU D 32 " pdb=" C LEU D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1091 0.048 - 0.097: 829 0.097 - 0.145: 354 0.145 - 0.193: 74 0.193 - 0.241: 27 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA ILE E 232 " pdb=" N ILE E 232 " pdb=" C ILE E 232 " pdb=" CB ILE E 232 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2372 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " -0.046 2.00e-02 2.50e+03 3.03e-02 1.60e+01 pdb=" CG PHE E 276 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 276 " 0.045 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE C 276 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE C 276 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 276 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE C 276 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 276 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 276 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 185 " 0.024 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP D 185 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 185 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 185 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP D 185 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 185 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP D 185 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 185 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 185 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 185 " -0.008 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1208 2.75 - 3.29: 17240 3.29 - 3.82: 27192 3.82 - 4.36: 35947 4.36 - 4.90: 57248 Nonbonded interactions: 138835 Sorted by model distance: nonbonded pdb=" OH TYR E 5 " pdb=" O ILE D 232 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR D 5 " pdb=" O ILE C 232 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 232 " pdb=" OH TYR C 5 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O ILE E 232 " model vdw 2.250 3.040 nonbonded pdb=" O ILE A 232 " pdb=" OH TYR B 5 " model vdw 2.256 3.040 ... (remaining 138830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'B' selection = chain 'D' selection = chain 'C' } 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=1.00 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: 4.790 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 : 0.013 0.059 16115 Z= 0.927 Angle : 1.249 6.855 21950 Z= 0.919 Chirality : 0.074 0.241 2375 Planarity : 0.007 0.033 2760 Dihedral : 14.396 89.329 5790 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 1870 helix: 1.20 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : 0.22 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG E 218 TYR 0.043 0.008 TYR A 97 PHE 0.046 0.007 PHE E 276 TRP 0.041 0.011 TRP D 185 HIS 0.011 0.005 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.01306 (16115) covalent geometry : angle 1.24893 (21950) hydrogen bonds : bond 0.10361 ( 975) hydrogen bonds : angle 4.73803 ( 2865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.7225 (pmt170) REVERT: E 25 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7013 (mpp-170) REVERT: E 57 GLU cc_start: 0.7963 (mp0) cc_final: 0.7734 (pt0) REVERT: E 119 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8436 (tt0) REVERT: E 325 MET cc_start: 0.9198 (mtp) cc_final: 0.8766 (mtp) REVERT: E 340 LYS cc_start: 0.6675 (mmtm) cc_final: 0.5868 (mtmt) REVERT: E 369 ASN cc_start: 0.7296 (m110) cc_final: 0.7090 (m-40) REVERT: B 57 GLU cc_start: 0.8092 (mp0) cc_final: 0.7644 (pt0) REVERT: B 331 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8690 (ttp-170) REVERT: D 25 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7314 (pmt170) REVERT: D 119 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8465 (tt0) REVERT: D 173 LYS cc_start: 0.8346 (mttp) cc_final: 0.8084 (mttp) REVERT: D 369 ASN cc_start: 0.7047 (m110) cc_final: 0.6802 (m-40) REVERT: C 25 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.6951 (mpp-170) REVERT: C 57 GLU cc_start: 0.7936 (mp0) cc_final: 0.7647 (pt0) REVERT: C 119 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8376 (tt0) REVERT: C 344 GLN cc_start: 0.8997 (mt0) cc_final: 0.8564 (mm110) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.7619 time to fit residues: 175.5675 Evaluate side-chains 165 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN B 96 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN D 96 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084702 restraints weight = 20839.395| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.83 r_work: 0.2850 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16115 Z= 0.142 Angle : 0.520 4.945 21950 Z= 0.285 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.031 2760 Dihedral : 5.875 80.600 2085 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.12 % Allowed : 6.31 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 1870 helix: 1.40 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.021 0.002 TYR D 97 PHE 0.028 0.002 PHE A 248 TRP 0.015 0.002 TRP A 309 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00305 (16115) covalent geometry : angle 0.51966 (21950) hydrogen bonds : bond 0.06020 ( 975) hydrogen bonds : angle 4.60431 ( 2865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.624 Fit side-chains REVERT: A 25 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.6677 (pmt170) REVERT: A 119 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: E 25 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.6657 (mpp-170) REVERT: E 119 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7612 (tt0) REVERT: E 268 GLU cc_start: 0.7816 (mp0) cc_final: 0.7552 (mp0) REVERT: E 290 VAL cc_start: 0.8213 (t) cc_final: 0.7854 (m) REVERT: E 293 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: E 325 MET cc_start: 0.9148 (mtp) cc_final: 0.8730 (mtp) REVERT: E 340 LYS cc_start: 0.6590 (mmtm) cc_final: 0.5549 (mtmt) REVERT: E 374 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: B 56 GLU cc_start: 0.7520 (tt0) cc_final: 0.7117 (tp30) REVERT: B 57 GLU cc_start: 0.7468 (mp0) cc_final: 0.7053 (pt0) REVERT: B 74 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8129 (pp30) REVERT: B 180 MET cc_start: 0.9001 (mmm) cc_final: 0.8705 (mmp) REVERT: B 374 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: D 25 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.6823 (pmt170) REVERT: D 119 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7800 (tt0) REVERT: D 355 ARG cc_start: 0.7356 (ttp-170) cc_final: 0.6926 (ttm110) REVERT: C 25 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.6412 (mpp-170) REVERT: C 56 GLU cc_start: 0.7398 (tt0) cc_final: 0.6974 (tp30) REVERT: C 119 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7745 (tt0) REVERT: C 290 VAL cc_start: 0.8434 (t) cc_final: 0.8129 (m) REVERT: C 344 GLN cc_start: 0.8704 (mt0) cc_final: 0.8079 (mm110) outliers start: 19 outliers final: 6 residues processed: 193 average time/residue: 0.6612 time to fit residues: 138.6914 Evaluate side-chains 175 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.081209 restraints weight = 21161.856| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.84 r_work: 0.2793 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16115 Z= 0.215 Angle : 0.555 9.307 21950 Z= 0.304 Chirality : 0.040 0.154 2375 Planarity : 0.005 0.051 2760 Dihedral : 5.815 81.636 2085 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.83 % Allowed : 7.61 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.18), residues: 1870 helix: 1.27 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 51 TYR 0.025 0.002 TYR D 97 PHE 0.027 0.002 PHE A 248 TRP 0.015 0.002 TRP A 309 HIS 0.006 0.002 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00510 (16115) covalent geometry : angle 0.55547 (21950) hydrogen bonds : bond 0.06665 ( 975) hydrogen bonds : angle 4.62248 ( 2865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.391 Fit side-chains REVERT: A 25 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.6616 (pmt170) REVERT: A 119 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: A 268 GLU cc_start: 0.7794 (mp0) cc_final: 0.7304 (mp0) REVERT: E 25 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.6560 (mpp-170) REVERT: E 119 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7627 (tt0) REVERT: E 268 GLU cc_start: 0.7884 (mp0) cc_final: 0.7528 (mp0) REVERT: E 293 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: E 325 MET cc_start: 0.9134 (mtp) cc_final: 0.8755 (mtp) REVERT: E 340 LYS cc_start: 0.6670 (mmtm) cc_final: 0.5565 (mtmt) REVERT: E 344 GLN cc_start: 0.8587 (mt0) cc_final: 0.8166 (mm110) REVERT: B 56 GLU cc_start: 0.7549 (tt0) cc_final: 0.7148 (tp30) REVERT: B 57 GLU cc_start: 0.7530 (mp0) cc_final: 0.7136 (pt0) REVERT: B 74 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8230 (pp30) REVERT: B 331 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.7911 (ttp-170) REVERT: B 344 GLN cc_start: 0.8799 (mt0) cc_final: 0.8483 (mt0) REVERT: B 374 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: D 25 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.6786 (pmt170) REVERT: D 119 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7691 (tt0) REVERT: D 355 ARG cc_start: 0.7338 (ttp-170) cc_final: 0.6972 (ttm110) REVERT: D 374 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6822 (mm-30) REVERT: C 25 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.6376 (mpp-170) REVERT: C 56 GLU cc_start: 0.7458 (tt0) cc_final: 0.6996 (pm20) REVERT: C 57 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6469 (pp20) REVERT: C 119 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7689 (tt0) REVERT: C 290 VAL cc_start: 0.8422 (t) cc_final: 0.8150 (m) REVERT: C 344 GLN cc_start: 0.8678 (mt0) cc_final: 0.7990 (mm110) REVERT: C 374 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6651 (mm-30) outliers start: 31 outliers final: 10 residues processed: 183 average time/residue: 0.6961 time to fit residues: 137.8560 Evaluate side-chains 169 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN E 96 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.083594 restraints weight = 20911.239| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.85 r_work: 0.2835 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16115 Z= 0.154 Angle : 0.497 8.066 21950 Z= 0.272 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.039 2760 Dihedral : 5.684 81.208 2085 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.01 % Allowed : 8.61 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 1870 helix: 1.35 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.021 0.001 TYR D 97 PHE 0.024 0.001 PHE B 248 TRP 0.014 0.002 TRP E 309 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00349 (16115) covalent geometry : angle 0.49670 (21950) hydrogen bonds : bond 0.05907 ( 975) hydrogen bonds : angle 4.53629 ( 2865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.654 Fit side-chains REVERT: A 25 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.6638 (pmt170) REVERT: A 119 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: A 268 GLU cc_start: 0.7841 (mp0) cc_final: 0.7358 (mp0) REVERT: E 25 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.6565 (mpp-170) REVERT: E 119 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7604 (tt0) REVERT: E 173 LYS cc_start: 0.7876 (mttp) cc_final: 0.7567 (mttm) REVERT: E 268 GLU cc_start: 0.7956 (mp0) cc_final: 0.7639 (mp0) REVERT: E 325 MET cc_start: 0.9111 (mtp) cc_final: 0.8777 (mtp) REVERT: E 340 LYS cc_start: 0.6666 (mmtm) cc_final: 0.5549 (mtmt) REVERT: E 344 GLN cc_start: 0.8531 (mt0) cc_final: 0.8184 (mm110) REVERT: B 56 GLU cc_start: 0.7542 (tt0) cc_final: 0.7175 (tp30) REVERT: B 57 GLU cc_start: 0.7496 (mp0) cc_final: 0.7099 (pt0) REVERT: B 74 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8162 (pp30) REVERT: B 180 MET cc_start: 0.8984 (mmm) cc_final: 0.8755 (mmp) REVERT: B 331 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8065 (tmm160) REVERT: B 344 GLN cc_start: 0.8777 (mt0) cc_final: 0.8468 (mt0) REVERT: B 374 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: D 25 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7548 (mmm-85) REVERT: D 119 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7758 (tt0) REVERT: D 355 ARG cc_start: 0.7289 (ttp-170) cc_final: 0.6926 (ttm110) REVERT: D 374 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6643 (mm-30) REVERT: C 25 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.6356 (mpp-170) REVERT: C 56 GLU cc_start: 0.7412 (tt0) cc_final: 0.6952 (pm20) REVERT: C 57 GLU cc_start: 0.6797 (pt0) cc_final: 0.6434 (pp20) REVERT: C 119 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7709 (tt0) REVERT: C 287 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.8011 (t-100) REVERT: C 290 VAL cc_start: 0.8399 (t) cc_final: 0.8142 (m) REVERT: C 344 GLN cc_start: 0.8672 (mt0) cc_final: 0.8049 (mm110) REVERT: C 374 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6622 (mm-30) outliers start: 34 outliers final: 11 residues processed: 188 average time/residue: 0.6651 time to fit residues: 136.1878 Evaluate side-chains 176 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.084140 restraints weight = 20951.629| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.86 r_work: 0.2857 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16115 Z= 0.144 Angle : 0.482 7.327 21950 Z= 0.264 Chirality : 0.037 0.153 2375 Planarity : 0.004 0.044 2760 Dihedral : 5.609 80.873 2085 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.24 % Allowed : 8.79 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 1870 helix: 1.43 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.04 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 51 TYR 0.020 0.001 TYR D 97 PHE 0.023 0.001 PHE B 248 TRP 0.013 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00321 (16115) covalent geometry : angle 0.48225 (21950) hydrogen bonds : bond 0.05761 ( 975) hydrogen bonds : angle 4.49523 ( 2865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.451 Fit side-chains REVERT: A 25 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.6566 (pmt170) REVERT: A 119 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: A 268 GLU cc_start: 0.7871 (mp0) cc_final: 0.7318 (mp0) REVERT: A 287 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (m-90) REVERT: E 25 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.6559 (mpp-170) REVERT: E 119 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7601 (tt0) REVERT: E 268 GLU cc_start: 0.7947 (mp0) cc_final: 0.7637 (mp0) REVERT: E 325 MET cc_start: 0.9109 (mtp) cc_final: 0.8800 (mtp) REVERT: E 344 GLN cc_start: 0.8559 (mt0) cc_final: 0.8186 (mm110) REVERT: E 374 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: B 56 GLU cc_start: 0.7543 (tt0) cc_final: 0.7178 (tp30) REVERT: B 57 GLU cc_start: 0.7570 (mp0) cc_final: 0.7145 (pt0) REVERT: B 74 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8154 (pp30) REVERT: B 180 MET cc_start: 0.8950 (mmm) cc_final: 0.8719 (mmp) REVERT: B 331 ARG cc_start: 0.8441 (ttp-170) cc_final: 0.8094 (tmm160) REVERT: B 344 GLN cc_start: 0.8769 (mt0) cc_final: 0.8453 (mt0) REVERT: B 374 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: D 25 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7557 (mmm-85) REVERT: D 119 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7686 (tt0) REVERT: D 355 ARG cc_start: 0.7298 (ttp-170) cc_final: 0.6949 (ttm110) REVERT: D 374 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6659 (mm-30) REVERT: C 25 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.6342 (mpp-170) REVERT: C 56 GLU cc_start: 0.7382 (tt0) cc_final: 0.6920 (pm20) REVERT: C 57 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6447 (pp20) REVERT: C 119 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7709 (tt0) REVERT: C 268 GLU cc_start: 0.7983 (mp0) cc_final: 0.7673 (mp0) REVERT: C 287 TRP cc_start: 0.8603 (OUTLIER) cc_final: 0.8082 (t-100) REVERT: C 290 VAL cc_start: 0.8378 (t) cc_final: 0.8122 (m) REVERT: C 344 GLN cc_start: 0.8665 (mt0) cc_final: 0.8019 (mm110) REVERT: C 374 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6604 (mm-30) outliers start: 38 outliers final: 14 residues processed: 186 average time/residue: 0.6323 time to fit residues: 128.0993 Evaluate side-chains 181 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.082952 restraints weight = 20875.642| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.83 r_work: 0.2827 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16115 Z= 0.172 Angle : 0.501 6.805 21950 Z= 0.275 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.045 2760 Dihedral : 5.629 81.333 2085 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.54 % Allowed : 8.85 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 130 TYR 0.023 0.002 TYR D 97 PHE 0.024 0.002 PHE B 248 TRP 0.013 0.002 TRP E 309 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00398 (16115) covalent geometry : angle 0.50097 (21950) hydrogen bonds : bond 0.06071 ( 975) hydrogen bonds : angle 4.52279 ( 2865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.643 Fit side-chains REVERT: A 25 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6543 (pmt170) REVERT: A 119 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: A 268 GLU cc_start: 0.7847 (mp0) cc_final: 0.7292 (mp0) REVERT: A 287 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.8354 (t-100) REVERT: E 25 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.6582 (mpp-170) REVERT: E 119 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7579 (tt0) REVERT: E 268 GLU cc_start: 0.7944 (mp0) cc_final: 0.7650 (mp0) REVERT: E 293 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: E 325 MET cc_start: 0.9122 (mtp) cc_final: 0.8695 (mtp) REVERT: E 344 GLN cc_start: 0.8570 (mt0) cc_final: 0.8193 (mm110) REVERT: E 374 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: B 56 GLU cc_start: 0.7549 (tt0) cc_final: 0.7226 (tp30) REVERT: B 57 GLU cc_start: 0.7590 (mp0) cc_final: 0.7162 (pt0) REVERT: B 74 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8188 (pp30) REVERT: B 180 MET cc_start: 0.8946 (mmm) cc_final: 0.8713 (mmp) REVERT: B 331 ARG cc_start: 0.8412 (ttp-170) cc_final: 0.8068 (tmm160) REVERT: B 344 GLN cc_start: 0.8801 (mt0) cc_final: 0.8501 (mt0) REVERT: B 374 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: D 25 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7604 (mmm-85) REVERT: D 119 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7693 (tt0) REVERT: D 287 TRP cc_start: 0.8758 (OUTLIER) cc_final: 0.8481 (t-100) REVERT: D 355 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6924 (ttm110) REVERT: D 374 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6640 (mm-30) REVERT: C 25 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.6356 (mpp-170) REVERT: C 56 GLU cc_start: 0.7402 (tt0) cc_final: 0.6926 (pm20) REVERT: C 57 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6456 (pp20) REVERT: C 119 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7709 (tt0) REVERT: C 287 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.8129 (t-100) REVERT: C 290 VAL cc_start: 0.8416 (t) cc_final: 0.8162 (m) REVERT: C 344 GLN cc_start: 0.8671 (mt0) cc_final: 0.8026 (mm110) REVERT: C 374 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6605 (mm-30) outliers start: 43 outliers final: 17 residues processed: 184 average time/residue: 0.6349 time to fit residues: 127.2032 Evaluate side-chains 183 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 68 optimal weight: 2.9990 chunk 145 optimal weight: 0.0060 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.086237 restraints weight = 20735.630| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.83 r_work: 0.2889 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16115 Z= 0.120 Angle : 0.459 6.229 21950 Z= 0.252 Chirality : 0.036 0.151 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.497 80.698 2085 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.77 % Allowed : 9.97 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.18), residues: 1870 helix: 1.61 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.01 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 130 TYR 0.016 0.001 TYR D 97 PHE 0.021 0.001 PHE B 248 TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00253 (16115) covalent geometry : angle 0.45920 (21950) hydrogen bonds : bond 0.05354 ( 975) hydrogen bonds : angle 4.43596 ( 2865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.717 Fit side-chains REVERT: A 25 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.6563 (pmt170) REVERT: A 119 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: A 268 GLU cc_start: 0.7856 (mp0) cc_final: 0.7399 (mp0) REVERT: E 25 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.6558 (mpp-170) REVERT: E 119 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7573 (tt0) REVERT: E 268 GLU cc_start: 0.7952 (mp0) cc_final: 0.7609 (mp0) REVERT: E 293 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: E 325 MET cc_start: 0.9106 (mtp) cc_final: 0.8706 (mtp) REVERT: E 344 GLN cc_start: 0.8520 (mt0) cc_final: 0.8160 (mm110) REVERT: E 374 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 56 GLU cc_start: 0.7462 (tt0) cc_final: 0.7189 (tp30) REVERT: B 57 GLU cc_start: 0.7596 (mp0) cc_final: 0.7141 (pt0) REVERT: B 74 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8141 (pp30) REVERT: B 180 MET cc_start: 0.8939 (mmm) cc_final: 0.8727 (mmp) REVERT: B 331 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8112 (tmm160) REVERT: B 344 GLN cc_start: 0.8820 (mt0) cc_final: 0.8526 (mt0) REVERT: B 374 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: D 25 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7587 (mmm-85) REVERT: D 61 MET cc_start: 0.7632 (tpt) cc_final: 0.6997 (ttp) REVERT: D 119 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7690 (tt0) REVERT: D 355 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.7001 (ttm110) REVERT: D 374 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6592 (mm-30) REVERT: C 25 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.6362 (mpp-170) REVERT: C 56 GLU cc_start: 0.7317 (tt0) cc_final: 0.6872 (pm20) REVERT: C 57 GLU cc_start: 0.6815 (pt0) cc_final: 0.6423 (pp20) REVERT: C 119 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7709 (tt0) REVERT: C 268 GLU cc_start: 0.8026 (mp0) cc_final: 0.7726 (mp0) REVERT: C 287 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8053 (t-100) REVERT: C 290 VAL cc_start: 0.8348 (t) cc_final: 0.8087 (m) REVERT: C 344 GLN cc_start: 0.8610 (mt0) cc_final: 0.7989 (mm110) REVERT: C 374 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6604 (mm-30) outliers start: 30 outliers final: 11 residues processed: 199 average time/residue: 0.6309 time to fit residues: 136.9057 Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 29 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.085445 restraints weight = 20813.312| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.84 r_work: 0.2872 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16115 Z= 0.133 Angle : 0.464 5.356 21950 Z= 0.255 Chirality : 0.036 0.152 2375 Planarity : 0.004 0.046 2760 Dihedral : 5.471 80.775 2085 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.89 % Allowed : 10.27 % Favored : 87.85 % 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 aren not related in a simple way. whole: 1.62 (0.18), residues: 1870 helix: 1.63 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.06 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.014 0.001 TYR E 236 PHE 0.021 0.001 PHE B 248 TRP 0.012 0.001 TRP E 309 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00292 (16115) covalent geometry : angle 0.46394 (21950) hydrogen bonds : bond 0.05517 ( 975) hydrogen bonds : angle 4.43505 ( 2865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.429 Fit side-chains REVERT: A 25 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.6554 (pmt170) REVERT: A 119 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 268 GLU cc_start: 0.7865 (mp0) cc_final: 0.7422 (mp0) REVERT: A 287 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.8309 (m-90) REVERT: E 25 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.6561 (mpp-170) REVERT: E 119 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7565 (tt0) REVERT: E 268 GLU cc_start: 0.7982 (mp0) cc_final: 0.7718 (mp0) REVERT: E 293 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: E 325 MET cc_start: 0.9102 (mtp) cc_final: 0.8694 (mtp) REVERT: E 344 GLN cc_start: 0.8531 (mt0) cc_final: 0.8171 (mm110) REVERT: E 374 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 56 GLU cc_start: 0.7416 (tt0) cc_final: 0.7150 (tp30) REVERT: B 57 GLU cc_start: 0.7590 (mp0) cc_final: 0.7135 (pt0) REVERT: B 74 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (pp30) REVERT: B 180 MET cc_start: 0.8935 (mmm) cc_final: 0.8723 (mmp) REVERT: B 331 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.8115 (tmm160) REVERT: B 344 GLN cc_start: 0.8820 (mt0) cc_final: 0.8522 (mt0) REVERT: B 374 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6090 (mp0) REVERT: D 25 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7584 (mmm-85) REVERT: D 61 MET cc_start: 0.7616 (tpt) cc_final: 0.6977 (ttp) REVERT: D 119 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7680 (tt0) REVERT: D 355 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.7023 (ttm110) REVERT: D 374 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6558 (mm-30) REVERT: C 25 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.6355 (mpp-170) REVERT: C 56 GLU cc_start: 0.7372 (tt0) cc_final: 0.6892 (pm20) REVERT: C 57 GLU cc_start: 0.6802 (pt0) cc_final: 0.6442 (pp20) REVERT: C 119 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7704 (tt0) REVERT: C 268 GLU cc_start: 0.8050 (mp0) cc_final: 0.7751 (mp0) REVERT: C 290 VAL cc_start: 0.8344 (t) cc_final: 0.8072 (m) REVERT: C 344 GLN cc_start: 0.8608 (mt0) cc_final: 0.7985 (mm110) REVERT: C 374 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6546 (mm-30) outliers start: 32 outliers final: 14 residues processed: 194 average time/residue: 0.6266 time to fit residues: 132.6511 Evaluate side-chains 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2468 > 50: distance: 139 - 157: 6.096 distance: 143 - 162: 4.659 distance: 147 - 169: 18.952 distance: 151 - 157: 5.641 distance: 152 - 177: 20.894 distance: 157 - 158: 5.758 distance: 158 - 159: 9.067 distance: 158 - 161: 13.165 distance: 159 - 160: 8.435 distance: 159 - 162: 7.476 distance: 162 - 163: 13.122 distance: 163 - 164: 21.613 distance: 163 - 166: 7.907 distance: 164 - 165: 11.130 distance: 164 - 169: 41.638 distance: 166 - 167: 11.390 distance: 166 - 168: 10.422 distance: 169 - 170: 10.744 distance: 170 - 171: 12.879 distance: 170 - 173: 15.692 distance: 171 - 172: 16.812 distance: 171 - 177: 18.139 distance: 173 - 174: 12.975 distance: 174 - 175: 18.614 distance: 174 - 176: 17.824 distance: 177 - 178: 11.687 distance: 178 - 179: 24.913 distance: 178 - 181: 18.661 distance: 179 - 180: 10.890 distance: 179 - 186: 13.401 distance: 181 - 182: 7.041 distance: 182 - 183: 7.907 distance: 183 - 184: 3.841 distance: 183 - 185: 8.929 distance: 186 - 187: 7.028 distance: 187 - 188: 8.715 distance: 187 - 190: 10.666 distance: 188 - 189: 16.242 distance: 188 - 194: 19.625 distance: 190 - 191: 20.899 distance: 191 - 192: 26.861 distance: 192 - 193: 28.411 distance: 194 - 195: 6.683 distance: 195 - 196: 6.816 distance: 195 - 198: 8.782 distance: 196 - 197: 11.839 distance: 196 - 204: 18.186 distance: 198 - 199: 12.912 distance: 199 - 200: 3.728 distance: 199 - 201: 3.746 distance: 200 - 202: 8.474 distance: 201 - 203: 7.002 distance: 202 - 203: 3.014 distance: 204 - 205: 10.196 distance: 205 - 206: 6.862 distance: 205 - 208: 9.574 distance: 206 - 207: 13.001 distance: 206 - 213: 16.530 distance: 208 - 209: 16.065 distance: 209 - 210: 11.444 distance: 210 - 211: 11.908 distance: 210 - 212: 12.748 distance: 213 - 214: 19.543 distance: 214 - 215: 17.164 distance: 214 - 217: 28.491 distance: 215 - 216: 21.100 distance: 215 - 221: 58.247 distance: 217 - 218: 18.429 distance: 218 - 219: 28.889 distance: 218 - 220: 11.182 distance: 221 - 222: 23.788 distance: 222 - 223: 11.239 distance: 222 - 225: 10.953 distance: 223 - 224: 10.318 distance: 223 - 229: 7.028 distance: 225 - 226: 21.894 distance: 226 - 227: 15.399 distance: 226 - 228: 21.249 distance: 229 - 230: 9.525 distance: 229 - 235: 16.110 distance: 230 - 231: 23.100 distance: 230 - 233: 10.099 distance: 231 - 232: 24.623 distance: 231 - 236: 9.442 distance: 233 - 234: 13.297 distance: 234 - 235: 16.305