Starting phenix.real_space_refine on Fri Aug 22 23:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja5_61290/08_2025/9ja5_61290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja5_61290/08_2025/9ja5_61290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ja5_61290/08_2025/9ja5_61290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja5_61290/08_2025/9ja5_61290.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja5_61290/08_2025/9ja5_61290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja5_61290/08_2025/9ja5_61290.cif" } resolution = 2.7 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= 0.022 sd= 1.765 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5148 2.51 5 N 1518 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 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: 8469 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1391 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.16, per 1000 atoms: 0.14 Number of scatterers: 8469 At special positions: 0 Unit cell: (85.6, 78.4, 210.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1761 8.00 N 1518 7.00 C 5148 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: 0.59 Conformation dependent library (CDL) restraints added in 304.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 72.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 211 through 275 removed outlier: 3.983A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.926A pdb=" N ARG A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU A 329 " --> pdb=" O ASP A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.653A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 275 removed outlier: 3.984A pdb=" N GLU B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 329' Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.653A pdb=" N SER B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 546 removed outlier: 3.877A pdb=" N PHE B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.832A pdb=" N SER C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.654A pdb=" N SER C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE C 546 " --> pdb=" O GLN C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 removed outlier: 3.918A pdb=" N LEU D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 329' Processing helix chain 'D' and resid 330 through 339 Processing helix chain 'D' and resid 342 through 347 removed outlier: 3.654A pdb=" N SER D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE D 546 " --> pdb=" O GLN D 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 248 " --> pdb=" O ARG E 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR E 314 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 329 removed outlier: 3.917A pdb=" N LEU E 329 " --> pdb=" O ASP E 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 329' Processing helix chain 'E' and resid 330 through 339 Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.654A pdb=" N SER E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE E 546 " --> pdb=" O GLN E 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 275 removed outlier: 3.983A pdb=" N GLU F 227 " --> pdb=" O LYS F 223 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN F 248 " --> pdb=" O ARG F 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 305 removed outlier: 3.833A pdb=" N SER F 305 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 318 removed outlier: 3.927A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 removed outlier: 3.918A pdb=" N LEU F 329 " --> pdb=" O ASP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 329' Processing helix chain 'F' and resid 330 through 339 Processing helix chain 'F' and resid 342 through 347 removed outlier: 3.653A pdb=" N SER F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 546 removed outlier: 3.876A pdb=" N PHE F 546 " --> pdb=" O GLN F 542 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1497 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: 0.99 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2739 1.33 - 1.45: 1018 1.45 - 1.56: 4637 1.56 - 1.68: 0 1.68 - 1.80: 78 Bond restraints: 8472 Sorted by residual: bond pdb=" C LEU E 306 " pdb=" N SER E 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.92e+00 bond pdb=" C LEU F 306 " pdb=" N SER F 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.86e+00 bond pdb=" C LEU A 306 " pdb=" N SER A 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.86e+00 bond pdb=" C LEU B 306 " pdb=" N SER B 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.84e+00 bond pdb=" C LEU C 306 " pdb=" N SER C 307 " ideal model delta sigma weight residual 1.333 1.287 0.045 1.73e-02 3.34e+03 6.83e+00 ... (remaining 8467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10499 1.79 - 3.58: 703 3.58 - 5.38: 110 5.38 - 7.17: 52 7.17 - 8.96: 42 Bond angle restraints: 11406 Sorted by residual: angle pdb=" C PHE E 285 " pdb=" CA PHE E 285 " pdb=" CB PHE E 285 " ideal model delta sigma weight residual 110.42 101.46 8.96 1.99e+00 2.53e-01 2.03e+01 angle pdb=" C PHE A 285 " pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " ideal model delta sigma weight residual 110.42 101.48 8.94 1.99e+00 2.53e-01 2.02e+01 angle pdb=" C PHE D 285 " pdb=" CA PHE D 285 " pdb=" CB PHE D 285 " ideal model delta sigma weight residual 110.42 101.49 8.93 1.99e+00 2.53e-01 2.01e+01 angle pdb=" C PHE C 285 " pdb=" CA PHE C 285 " pdb=" CB PHE C 285 " ideal model delta sigma weight residual 110.42 101.50 8.92 1.99e+00 2.53e-01 2.01e+01 angle pdb=" C PHE B 285 " pdb=" CA PHE B 285 " pdb=" CB PHE B 285 " ideal model delta sigma weight residual 110.42 101.52 8.90 1.99e+00 2.53e-01 2.00e+01 ... (remaining 11401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.19: 4433 14.19 - 28.38: 679 28.38 - 42.56: 144 42.56 - 56.75: 24 56.75 - 70.94: 18 Dihedral angle restraints: 5298 sinusoidal: 2322 harmonic: 2976 Sorted by residual: dihedral pdb=" CA PHE C 285 " pdb=" C PHE C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE D 285 " pdb=" C PHE D 285 " pdb=" N ASN D 286 " pdb=" CA ASN D 286 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE B 285 " pdb=" C PHE B 285 " pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 419 0.037 - 0.073: 535 0.073 - 0.110: 171 0.110 - 0.146: 63 0.146 - 0.183: 36 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA GLU E 238 " pdb=" N GLU E 238 " pdb=" C GLU E 238 " pdb=" CB GLU E 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA SER A 307 " pdb=" N SER A 307 " pdb=" C SER A 307 " pdb=" CB SER A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU A 238 " pdb=" N GLU A 238 " pdb=" C GLU A 238 " pdb=" CB GLU A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 1221 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 285 " -0.035 2.00e-02 2.50e+03 2.92e-02 1.50e+01 pdb=" CG PHE D 285 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE D 285 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 285 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 285 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 285 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 285 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 285 " 0.034 2.00e-02 2.50e+03 2.92e-02 1.49e+01 pdb=" CG PHE C 285 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE C 285 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 285 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 285 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 285 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 285 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 285 " -0.034 2.00e-02 2.50e+03 2.92e-02 1.49e+01 pdb=" CG PHE F 285 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE F 285 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE F 285 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 285 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 285 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 285 " -0.005 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 316 2.67 - 3.23: 8692 3.23 - 3.79: 12514 3.79 - 4.34: 16572 4.34 - 4.90: 27000 Nonbonded interactions: 65094 Sorted by model distance: nonbonded pdb=" OE2 GLU A 309 " pdb=" O HOH A 701 " model vdw 2.117 3.040 nonbonded pdb=" OE2 GLU D 309 " pdb=" O HOH D 701 " model vdw 2.119 3.040 nonbonded pdb=" O SER A 307 " pdb=" OG SER A 307 " model vdw 2.126 3.040 nonbonded pdb=" O SER D 307 " pdb=" OG SER D 307 " model vdw 2.126 3.040 nonbonded pdb=" O SER F 307 " pdb=" OG SER F 307 " model vdw 2.126 3.040 ... (remaining 65089 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 3.650 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.066 8472 Z= 0.605 Angle : 1.154 8.958 11406 Z= 0.626 Chirality : 0.064 0.183 1224 Planarity : 0.005 0.029 1518 Dihedral : 14.299 70.938 3342 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.73 (0.25), residues: 978 helix: -0.98 (0.18), residues: 714 sheet: None (None), residues: 0 loop : -3.96 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 215 TYR 0.026 0.004 TYR B 314 PHE 0.068 0.005 PHE D 285 TRP 0.051 0.006 TRP D 221 Details of bonding type rmsd covalent geometry : bond 0.01439 ( 8472) covalent geometry : angle 1.15352 (11406) hydrogen bonds : bond 0.17848 ( 499) hydrogen bonds : angle 5.65006 ( 1497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.375 Fit side-chains REVERT: A 245 ASP cc_start: 0.7624 (m-30) cc_final: 0.7160 (t0) REVERT: A 301 GLU cc_start: 0.8565 (mp0) cc_final: 0.8319 (mp0) REVERT: A 308 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8698 (tp30) REVERT: A 309 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 323 ASP cc_start: 0.8256 (t0) cc_final: 0.7920 (t0) REVERT: A 527 LEU cc_start: 0.9275 (mp) cc_final: 0.9040 (mp) REVERT: A 531 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 245 ASP cc_start: 0.7507 (m-30) cc_final: 0.7264 (t0) REVERT: B 309 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 323 ASP cc_start: 0.8209 (t0) cc_final: 0.8009 (t0) REVERT: C 245 ASP cc_start: 0.7803 (m-30) cc_final: 0.6917 (OUTLIER) REVERT: C 309 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7433 (tm-30) REVERT: C 323 ASP cc_start: 0.8037 (t0) cc_final: 0.7544 (t0) REVERT: C 326 ASP cc_start: 0.8389 (t0) cc_final: 0.7931 (t0) REVERT: D 245 ASP cc_start: 0.7634 (m-30) cc_final: 0.7380 (OUTLIER) REVERT: D 309 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 323 ASP cc_start: 0.8208 (t0) cc_final: 0.7863 (t0) REVERT: D 326 ASP cc_start: 0.8369 (t0) cc_final: 0.8098 (t70) REVERT: D 527 LEU cc_start: 0.9139 (mp) cc_final: 0.8805 (mt) REVERT: D 531 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7471 (mt-10) REVERT: E 324 GLU cc_start: 0.8450 (tp30) cc_final: 0.7783 (tp30) REVERT: E 534 GLU cc_start: 0.7828 (tp30) cc_final: 0.7434 (tp30) REVERT: F 245 ASP cc_start: 0.7919 (m-30) cc_final: 0.7253 (OUTLIER) REVERT: F 309 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 323 ASP cc_start: 0.8135 (t0) cc_final: 0.7733 (t0) REVERT: F 326 ASP cc_start: 0.8488 (t0) cc_final: 0.8106 (t0) outliers start: 0 outliers final: 3 residues processed: 249 average time/residue: 0.7072 time to fit residues: 184.2164 Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.161283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117643 restraints weight = 9268.836| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.66 r_work: 0.3245 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8472 Z= 0.169 Angle : 0.677 7.378 11406 Z= 0.356 Chirality : 0.039 0.159 1224 Planarity : 0.004 0.040 1518 Dihedral : 4.938 18.431 1134 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.03 % Allowed : 14.10 % Favored : 83.87 % 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: -0.74 (0.27), residues: 978 helix: 0.60 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -3.25 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 222 TYR 0.008 0.001 TYR D 314 PHE 0.026 0.002 PHE F 285 TRP 0.031 0.003 TRP C 221 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8472) covalent geometry : angle 0.67684 (11406) hydrogen bonds : bond 0.08880 ( 499) hydrogen bonds : angle 4.03317 ( 1497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.356 Fit side-chains REVERT: A 245 ASP cc_start: 0.7470 (m-30) cc_final: 0.6958 (OUTLIER) REVERT: A 309 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 323 ASP cc_start: 0.7802 (t0) cc_final: 0.7289 (t0) REVERT: A 527 LEU cc_start: 0.9133 (mp) cc_final: 0.8885 (mp) REVERT: B 245 ASP cc_start: 0.7460 (m-30) cc_final: 0.7065 (t0) REVERT: B 323 ASP cc_start: 0.7881 (t0) cc_final: 0.7501 (t0) REVERT: C 245 ASP cc_start: 0.7596 (m-30) cc_final: 0.6800 (OUTLIER) REVERT: C 309 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6686 (tm-30) REVERT: C 316 LYS cc_start: 0.7559 (mttt) cc_final: 0.7223 (mttm) REVERT: C 323 ASP cc_start: 0.7667 (t0) cc_final: 0.7203 (t0) REVERT: C 326 ASP cc_start: 0.7552 (t0) cc_final: 0.7087 (t0) REVERT: D 245 ASP cc_start: 0.7636 (m-30) cc_final: 0.7237 (OUTLIER) REVERT: D 309 GLU cc_start: 0.7599 (tm-30) cc_final: 0.6931 (tm-30) REVERT: D 323 ASP cc_start: 0.7739 (t0) cc_final: 0.7261 (t0) REVERT: E 301 GLU cc_start: 0.8491 (mp0) cc_final: 0.8272 (mp0) REVERT: E 534 GLU cc_start: 0.7483 (tp30) cc_final: 0.7005 (tp30) REVERT: F 245 ASP cc_start: 0.7867 (m-30) cc_final: 0.7120 (t0) REVERT: F 309 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6653 (tm-30) REVERT: F 316 LYS cc_start: 0.7545 (mttt) cc_final: 0.7333 (mttm) REVERT: F 323 ASP cc_start: 0.7839 (t0) cc_final: 0.7259 (t0) REVERT: F 326 ASP cc_start: 0.7719 (t0) cc_final: 0.7159 (t0) outliers start: 19 outliers final: 8 residues processed: 239 average time/residue: 0.7127 time to fit residues: 178.9494 Evaluate side-chains 222 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 217 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 225 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116214 restraints weight = 9291.158| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.65 r_work: 0.3223 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8472 Z= 0.166 Angle : 0.632 7.003 11406 Z= 0.327 Chirality : 0.039 0.156 1224 Planarity : 0.004 0.036 1518 Dihedral : 4.545 22.538 1134 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.71 % Allowed : 20.09 % Favored : 78.21 % 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: 0.12 (0.28), residues: 978 helix: 1.18 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.85 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 222 TYR 0.007 0.001 TYR B 314 PHE 0.025 0.002 PHE F 285 TRP 0.040 0.002 TRP B 221 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8472) covalent geometry : angle 0.63184 (11406) hydrogen bonds : bond 0.08278 ( 499) hydrogen bonds : angle 3.85914 ( 1497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.253 Fit side-chains REVERT: A 245 ASP cc_start: 0.7402 (m-30) cc_final: 0.6910 (t0) REVERT: A 308 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8686 (tm-30) REVERT: A 309 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6815 (tm-30) REVERT: A 323 ASP cc_start: 0.7760 (t0) cc_final: 0.7207 (t0) REVERT: B 245 ASP cc_start: 0.7384 (m-30) cc_final: 0.7152 (t0) REVERT: B 308 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8640 (tm-30) REVERT: B 309 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6475 (tm-30) REVERT: B 323 ASP cc_start: 0.7898 (t0) cc_final: 0.7452 (t0) REVERT: C 221 TRP cc_start: 0.6712 (t60) cc_final: 0.6240 (t60) REVERT: C 245 ASP cc_start: 0.7512 (m-30) cc_final: 0.6777 (t0) REVERT: C 309 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6668 (tm-30) REVERT: C 323 ASP cc_start: 0.7674 (t0) cc_final: 0.7051 (t0) REVERT: D 245 ASP cc_start: 0.7598 (m-30) cc_final: 0.7207 (t0) REVERT: D 308 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8669 (tm-30) REVERT: D 309 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6696 (tm-30) REVERT: D 323 ASP cc_start: 0.7788 (t0) cc_final: 0.7238 (t0) REVERT: E 309 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6569 (tm-30) REVERT: E 323 ASP cc_start: 0.7885 (t0) cc_final: 0.7434 (t0) REVERT: F 245 ASP cc_start: 0.7827 (m-30) cc_final: 0.7073 (t0) REVERT: F 309 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6689 (tm-30) REVERT: F 323 ASP cc_start: 0.7862 (t0) cc_final: 0.7321 (t0) REVERT: F 326 ASP cc_start: 0.7577 (t0) cc_final: 0.7044 (t0) outliers start: 16 outliers final: 12 residues processed: 232 average time/residue: 0.6637 time to fit residues: 161.6771 Evaluate side-chains 220 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117165 restraints weight = 9422.928| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.69 r_work: 0.3227 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8472 Z= 0.160 Angle : 0.615 9.341 11406 Z= 0.314 Chirality : 0.038 0.152 1224 Planarity : 0.004 0.031 1518 Dihedral : 4.399 22.990 1134 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.03 % Allowed : 21.15 % Favored : 76.82 % 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: 1.05 (0.28), residues: 978 helix: 1.99 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 222 TYR 0.006 0.001 TYR D 348 PHE 0.021 0.002 PHE D 285 TRP 0.053 0.002 TRP B 221 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8472) covalent geometry : angle 0.61505 (11406) hydrogen bonds : bond 0.07856 ( 499) hydrogen bonds : angle 3.75399 ( 1497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7414 (m-30) cc_final: 0.6890 (t0) REVERT: A 308 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 309 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 323 ASP cc_start: 0.7747 (t0) cc_final: 0.7210 (t0) REVERT: B 244 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7614 (ttp80) REVERT: B 245 ASP cc_start: 0.7371 (m-30) cc_final: 0.6983 (t0) REVERT: B 249 ASP cc_start: 0.7912 (m-30) cc_final: 0.7678 (m-30) REVERT: B 308 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 309 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6346 (tm-30) REVERT: B 323 ASP cc_start: 0.7893 (t0) cc_final: 0.7427 (t0) REVERT: C 221 TRP cc_start: 0.6585 (t60) cc_final: 0.6127 (t60) REVERT: C 245 ASP cc_start: 0.7472 (m-30) cc_final: 0.6716 (t0) REVERT: C 249 ASP cc_start: 0.8032 (m-30) cc_final: 0.7726 (m-30) REVERT: C 308 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 309 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6526 (tm-30) REVERT: C 323 ASP cc_start: 0.7694 (t0) cc_final: 0.7112 (t0) REVERT: D 245 ASP cc_start: 0.7561 (m-30) cc_final: 0.7148 (t0) REVERT: D 308 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 309 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6569 (tm-30) REVERT: D 323 ASP cc_start: 0.7728 (t0) cc_final: 0.7167 (t0) REVERT: E 241 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7575 (t0) REVERT: E 308 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8546 (tm-30) REVERT: F 245 ASP cc_start: 0.7801 (m-30) cc_final: 0.7064 (t0) REVERT: F 308 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8644 (tm-30) REVERT: F 309 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6549 (tm-30) REVERT: F 323 ASP cc_start: 0.7874 (t0) cc_final: 0.7347 (t0) outliers start: 19 outliers final: 11 residues processed: 222 average time/residue: 0.7249 time to fit residues: 169.0062 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115818 restraints weight = 9461.227| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.72 r_work: 0.3209 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8472 Z= 0.168 Angle : 0.617 9.000 11406 Z= 0.314 Chirality : 0.038 0.151 1224 Planarity : 0.004 0.029 1518 Dihedral : 4.337 26.226 1134 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.56 % Allowed : 22.12 % Favored : 75.32 % 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 (0.29), residues: 978 helix: 2.00 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.42 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.006 0.001 TYR D 348 PHE 0.022 0.002 PHE F 285 TRP 0.038 0.002 TRP B 221 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8472) covalent geometry : angle 0.61665 (11406) hydrogen bonds : bond 0.07890 ( 499) hydrogen bonds : angle 3.72515 ( 1497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7415 (m-30) cc_final: 0.6893 (t0) REVERT: A 308 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 309 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 323 ASP cc_start: 0.7677 (t0) cc_final: 0.7153 (t0) REVERT: B 244 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7688 (ttp80) REVERT: B 308 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 309 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6632 (tm-30) REVERT: C 211 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7900 (pp-130) REVERT: C 245 ASP cc_start: 0.7482 (m-30) cc_final: 0.6752 (t0) REVERT: C 308 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8521 (tm-30) REVERT: C 309 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6584 (tm-30) REVERT: C 323 ASP cc_start: 0.7693 (t0) cc_final: 0.7113 (t0) REVERT: D 245 ASP cc_start: 0.7563 (m-30) cc_final: 0.7128 (t0) REVERT: D 308 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8489 (tm-30) REVERT: D 309 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6555 (tm-30) REVERT: D 323 ASP cc_start: 0.7728 (t0) cc_final: 0.7144 (t0) REVERT: E 241 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7680 (t0) REVERT: E 308 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 323 ASP cc_start: 0.7870 (t0) cc_final: 0.7364 (t0) REVERT: F 211 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7772 (pp-130) REVERT: F 245 ASP cc_start: 0.7782 (m-30) cc_final: 0.7022 (t0) REVERT: F 308 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8688 (tm-30) REVERT: F 323 ASP cc_start: 0.7844 (t0) cc_final: 0.7341 (t0) outliers start: 24 outliers final: 13 residues processed: 219 average time/residue: 0.6796 time to fit residues: 156.7085 Evaluate side-chains 215 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117523 restraints weight = 9393.996| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.71 r_work: 0.3230 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8472 Z= 0.157 Angle : 0.619 9.652 11406 Z= 0.312 Chirality : 0.038 0.152 1224 Planarity : 0.004 0.046 1518 Dihedral : 4.316 26.366 1134 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.78 % Allowed : 22.22 % Favored : 75.00 % 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: 1.61 (0.28), residues: 978 helix: 2.41 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.00 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.005 0.001 TYR F 348 PHE 0.019 0.002 PHE F 285 TRP 0.058 0.002 TRP A 221 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8472) covalent geometry : angle 0.61907 (11406) hydrogen bonds : bond 0.07605 ( 499) hydrogen bonds : angle 3.67823 ( 1497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.353 Fit side-chains REVERT: A 245 ASP cc_start: 0.7418 (m-30) cc_final: 0.6887 (t0) REVERT: A 308 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 309 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6610 (tm-30) REVERT: A 323 ASP cc_start: 0.7661 (t0) cc_final: 0.7079 (t0) REVERT: B 227 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: B 308 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 309 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6642 (tm-30) REVERT: C 211 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7926 (pp-130) REVERT: C 245 ASP cc_start: 0.7448 (m-30) cc_final: 0.6658 (t0) REVERT: C 249 ASP cc_start: 0.8016 (m-30) cc_final: 0.7610 (m-30) REVERT: C 308 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 309 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6543 (tm-30) REVERT: C 323 ASP cc_start: 0.7663 (t0) cc_final: 0.7078 (t0) REVERT: D 308 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8497 (tm-30) REVERT: D 309 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6503 (tm-30) REVERT: D 323 ASP cc_start: 0.7711 (t0) cc_final: 0.7141 (t0) REVERT: E 241 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7503 (t0) REVERT: E 308 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8446 (tm-30) REVERT: F 211 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7739 (pp-130) REVERT: F 245 ASP cc_start: 0.7778 (m-30) cc_final: 0.7022 (t0) REVERT: F 308 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8600 (tm-30) REVERT: F 323 ASP cc_start: 0.7845 (t0) cc_final: 0.7332 (t0) outliers start: 26 outliers final: 14 residues processed: 219 average time/residue: 0.7009 time to fit residues: 161.3985 Evaluate side-chains 217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 40 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: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113484 restraints weight = 9588.489| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.74 r_work: 0.3174 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8472 Z= 0.196 Angle : 0.681 10.254 11406 Z= 0.339 Chirality : 0.040 0.167 1224 Planarity : 0.004 0.038 1518 Dihedral : 4.503 27.049 1134 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.35 % Allowed : 22.86 % Favored : 74.79 % 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: 1.40 (0.28), residues: 978 helix: 2.11 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.29 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 222 TYR 0.006 0.001 TYR B 318 PHE 0.025 0.002 PHE F 285 TRP 0.053 0.003 TRP A 221 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8472) covalent geometry : angle 0.68054 (11406) hydrogen bonds : bond 0.08193 ( 499) hydrogen bonds : angle 3.79285 ( 1497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.359 Fit side-chains REVERT: A 245 ASP cc_start: 0.7478 (m-30) cc_final: 0.6920 (t0) REVERT: A 308 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 309 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6606 (tm-30) REVERT: A 323 ASP cc_start: 0.7662 (t0) cc_final: 0.7120 (t0) REVERT: B 296 ARG cc_start: 0.8581 (mmp80) cc_final: 0.8274 (mmp-170) REVERT: B 308 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 309 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6583 (tm-30) REVERT: C 211 MET cc_start: 0.7838 (pp-130) cc_final: 0.7598 (pp-130) REVERT: C 237 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.7186 (mmt90) REVERT: C 245 ASP cc_start: 0.7501 (m-30) cc_final: 0.6754 (t0) REVERT: C 308 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8452 (tm-30) REVERT: C 309 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6562 (tm-30) REVERT: C 323 ASP cc_start: 0.7694 (t0) cc_final: 0.7091 (t0) REVERT: D 308 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8473 (tm-30) REVERT: D 309 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6603 (tm-30) REVERT: D 323 ASP cc_start: 0.7712 (t0) cc_final: 0.7167 (t0) REVERT: E 241 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7687 (t0) REVERT: E 308 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8414 (tm-30) REVERT: E 323 ASP cc_start: 0.7828 (t0) cc_final: 0.7335 (t0) REVERT: F 211 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7781 (pp-130) REVERT: F 245 ASP cc_start: 0.7853 (m-30) cc_final: 0.7054 (t0) REVERT: F 308 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8573 (tm-30) REVERT: F 309 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6423 (tm-30) REVERT: F 323 ASP cc_start: 0.7862 (t0) cc_final: 0.7351 (t0) outliers start: 22 outliers final: 14 residues processed: 215 average time/residue: 0.6898 time to fit residues: 156.1394 Evaluate side-chains 211 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115459 restraints weight = 9427.635| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.75 r_work: 0.3202 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8472 Z= 0.173 Angle : 0.664 10.020 11406 Z= 0.330 Chirality : 0.038 0.191 1224 Planarity : 0.004 0.039 1518 Dihedral : 4.440 29.787 1134 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.92 % Allowed : 23.18 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.73 (0.28), residues: 978 helix: 2.50 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 215 TYR 0.005 0.001 TYR F 348 PHE 0.021 0.002 PHE F 285 TRP 0.057 0.003 TRP B 221 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8472) covalent geometry : angle 0.66404 (11406) hydrogen bonds : bond 0.07856 ( 499) hydrogen bonds : angle 3.74276 ( 1497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.457 Fit side-chains REVERT: A 245 ASP cc_start: 0.7452 (m-30) cc_final: 0.6906 (t0) REVERT: A 308 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 309 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6548 (tm-30) REVERT: A 323 ASP cc_start: 0.7626 (t0) cc_final: 0.7099 (t0) REVERT: B 296 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8277 (mmp-170) REVERT: B 308 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 309 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6632 (tm-30) REVERT: B 323 ASP cc_start: 0.7895 (t0) cc_final: 0.7394 (t0) REVERT: C 211 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7386 (pp-130) REVERT: C 245 ASP cc_start: 0.7484 (m-30) cc_final: 0.6730 (t0) REVERT: C 249 ASP cc_start: 0.8051 (m-30) cc_final: 0.7776 (m-30) REVERT: C 308 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 309 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6515 (tm-30) REVERT: C 323 ASP cc_start: 0.7658 (t0) cc_final: 0.7093 (t0) REVERT: D 308 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8495 (tm-30) REVERT: D 309 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6505 (tm-30) REVERT: D 323 ASP cc_start: 0.7697 (t0) cc_final: 0.7149 (t0) REVERT: E 241 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7437 (t0) REVERT: E 308 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8393 (tm-30) REVERT: F 211 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7759 (pp-130) REVERT: F 245 ASP cc_start: 0.7821 (m-30) cc_final: 0.7035 (t0) REVERT: F 308 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8568 (tm-30) REVERT: F 309 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6376 (tm-30) REVERT: F 323 ASP cc_start: 0.7814 (t0) cc_final: 0.7311 (t0) outliers start: 18 outliers final: 12 residues processed: 206 average time/residue: 0.7326 time to fit residues: 158.5683 Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117591 restraints weight = 9448.186| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.73 r_work: 0.3228 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8472 Z= 0.154 Angle : 0.656 10.225 11406 Z= 0.325 Chirality : 0.038 0.188 1224 Planarity : 0.004 0.049 1518 Dihedral : 4.328 28.919 1134 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.71 % Allowed : 23.29 % Favored : 75.00 % 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: 1.71 (0.29), residues: 978 helix: 2.35 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.21 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 222 TYR 0.005 0.001 TYR F 348 PHE 0.019 0.002 PHE F 285 TRP 0.054 0.003 TRP B 221 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8472) covalent geometry : angle 0.65566 (11406) hydrogen bonds : bond 0.07466 ( 499) hydrogen bonds : angle 3.68761 ( 1497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7453 (m-30) cc_final: 0.6898 (t0) REVERT: A 308 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 309 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6529 (tm-30) REVERT: A 323 ASP cc_start: 0.7617 (t0) cc_final: 0.7048 (t0) REVERT: B 296 ARG cc_start: 0.8567 (mmp80) cc_final: 0.8253 (mmp-170) REVERT: B 308 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 309 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6628 (tm-30) REVERT: C 211 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7274 (pp-130) REVERT: C 249 ASP cc_start: 0.8008 (m-30) cc_final: 0.7722 (m-30) REVERT: C 308 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8420 (tm-30) REVERT: C 309 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6520 (tm-30) REVERT: C 323 ASP cc_start: 0.7651 (t0) cc_final: 0.7083 (t0) REVERT: D 308 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 309 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6845 (tp30) REVERT: D 323 ASP cc_start: 0.7687 (t0) cc_final: 0.7144 (t0) REVERT: E 241 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7645 (t0) REVERT: E 286 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7819 (p0) REVERT: E 308 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8392 (tm-30) REVERT: E 323 ASP cc_start: 0.7812 (t0) cc_final: 0.7342 (t0) REVERT: F 211 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7735 (pp-130) REVERT: F 245 ASP cc_start: 0.7801 (m-30) cc_final: 0.7021 (t0) REVERT: F 308 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8558 (tm-30) REVERT: F 323 ASP cc_start: 0.7810 (t0) cc_final: 0.7297 (t0) outliers start: 16 outliers final: 8 residues processed: 209 average time/residue: 0.7017 time to fit residues: 154.2973 Evaluate side-chains 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 69.82 > 50: distance: 31 - 37: 10.836 distance: 37 - 38: 12.174 distance: 37 - 43: 6.913 distance: 38 - 39: 14.354 distance: 38 - 41: 4.212 distance: 39 - 40: 27.559 distance: 39 - 44: 19.429 distance: 41 - 42: 11.466 distance: 42 - 43: 9.742 distance: 44 - 45: 3.199 distance: 45 - 46: 15.447 distance: 45 - 48: 15.994 distance: 46 - 47: 21.430 distance: 46 - 52: 36.195 distance: 48 - 49: 9.530 distance: 52 - 53: 24.851 distance: 52 - 58: 24.923 distance: 53 - 54: 54.813 distance: 53 - 56: 9.670 distance: 54 - 55: 20.276 distance: 59 - 60: 8.451 distance: 60 - 61: 18.436 distance: 60 - 63: 26.795 distance: 61 - 62: 45.556 distance: 61 - 67: 9.854 distance: 63 - 64: 24.412 distance: 64 - 66: 48.497 distance: 67 - 68: 9.158 distance: 68 - 69: 10.012 distance: 69 - 70: 41.454 distance: 69 - 75: 20.286 distance: 71 - 72: 19.765 distance: 72 - 73: 8.846 distance: 72 - 74: 12.308 distance: 75 - 76: 13.546 distance: 75 - 81: 16.937 distance: 76 - 77: 17.974 distance: 77 - 78: 10.721 distance: 77 - 82: 15.312 distance: 79 - 80: 26.289 distance: 80 - 81: 4.870 distance: 82 - 83: 16.390 distance: 83 - 84: 5.150 distance: 83 - 86: 22.331 distance: 84 - 85: 10.266 distance: 84 - 93: 4.322 distance: 86 - 87: 34.576 distance: 87 - 88: 24.355 distance: 88 - 89: 9.003 distance: 89 - 90: 19.174 distance: 90 - 91: 10.090 distance: 90 - 92: 30.419 distance: 93 - 94: 25.076 distance: 94 - 95: 17.901 distance: 94 - 97: 8.960 distance: 95 - 96: 16.343 distance: 95 - 101: 17.023 distance: 97 - 98: 30.280 distance: 97 - 99: 21.397 distance: 98 - 100: 10.159 distance: 101 - 102: 8.579 distance: 102 - 103: 7.682 distance: 102 - 105: 7.488 distance: 103 - 104: 19.926 distance: 103 - 108: 20.150 distance: 105 - 106: 9.910 distance: 105 - 107: 22.319 distance: 108 - 109: 7.471 distance: 109 - 110: 17.189 distance: 109 - 112: 16.482 distance: 110 - 111: 47.518 distance: 110 - 119: 21.623 distance: 111 - 142: 26.197 distance: 112 - 113: 27.631 distance: 113 - 114: 26.108 distance: 115 - 116: 8.974 distance: 116 - 117: 22.919 distance: 116 - 118: 15.846