Starting phenix.real_space_refine on Tue Feb 3 23:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s2t_19683/02_2026/8s2t_19683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s2t_19683/02_2026/8s2t_19683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s2t_19683/02_2026/8s2t_19683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s2t_19683/02_2026/8s2t_19683.map" model { file = "/net/cci-nas-00/data/ceres_data/8s2t_19683/02_2026/8s2t_19683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s2t_19683/02_2026/8s2t_19683.cif" } resolution = 3.3 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= -0.000 sd= 0.001 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 53 5.16 5 C 5045 2.51 5 N 1400 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7955 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1673 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain breaks: 4 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2269 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.27, per 1000 atoms: 0.16 Number of scatterers: 7955 At special positions: 0 Unit cell: (82.7105, 100.839, 129.164, 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 53 16.00 O 1457 8.00 N 1400 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 216 " distance=2.03 Simple disulfide: pdb=" SG CYS R 209 " - pdb=" SG CYS R 215 " distance=2.03 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: 0.53 Conformation dependent library (CDL) restraints added in 286.8 milliseconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 43.4% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 3.655A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 4.002A pdb=" N ASN A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 317 through 336 Processing helix chain 'A' and resid 354 through 377 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 56 through 86 Processing helix chain 'R' and resid 87 through 90 Processing helix chain 'R' and resid 92 through 111 removed outlier: 3.753A pdb=" N PHE R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 121 removed outlier: 4.130A pdb=" N THR R 117 " --> pdb=" O PRO R 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE R 118 " --> pdb=" O PHE R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 162 removed outlier: 3.914A pdb=" N CYS R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 171 through 188 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'R' and resid 203 through 209 Processing helix chain 'R' and resid 221 through 233 Processing helix chain 'R' and resid 233 through 263 removed outlier: 4.137A pdb=" N CYS R 261 " --> pdb=" O LYS R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 349 Proline residue: R 339 - end of helix Processing helix chain 'R' and resid 355 through 368 Processing helix chain 'R' and resid 368 through 373 Processing helix chain 'R' and resid 374 through 376 No H-bonds generated for 'chain 'R' and resid 374 through 376' Processing helix chain 'R' and resid 380 through 392 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.207A pdb=" N HIS A 41 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE A 208 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU A 43 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 273 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HIS A 348 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 275 " --> pdb=" O HIS A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.724A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.298A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.396A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.908A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.356A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.705A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1203 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: 1.27 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1383 1.30 - 1.44: 2383 1.44 - 1.57: 4235 1.57 - 1.70: 47 1.70 - 1.84: 71 Bond restraints: 8119 Sorted by residual: bond pdb=" CB HIS B 225 " pdb=" CG HIS B 225 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.15e+01 bond pdb=" NE ARG C 62 " pdb=" CZ ARG C 62 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.56e+01 bond pdb=" CB ARG A 218 " pdb=" CG ARG A 218 " ideal model delta sigma weight residual 1.520 1.337 0.183 3.00e-02 1.11e+03 3.73e+01 bond pdb=" CB ASP B 205 " pdb=" CG ASP B 205 " ideal model delta sigma weight residual 1.516 1.365 0.151 2.50e-02 1.60e+03 3.63e+01 bond pdb=" CB HIS B 142 " pdb=" CG HIS B 142 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.57e+01 ... (remaining 8114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 9584 2.60 - 5.21: 1228 5.21 - 7.81: 166 7.81 - 10.42: 18 10.42 - 13.02: 3 Bond angle restraints: 10999 Sorted by residual: angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 114.04 101.02 13.02 1.24e+00 6.50e-01 1.10e+02 angle pdb=" C SER R 162 " pdb=" N PRO R 163 " pdb=" CA PRO R 163 " ideal model delta sigma weight residual 119.56 128.23 -8.67 1.01e+00 9.80e-01 7.37e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 109.58 99.00 10.58 1.29e+00 6.01e-01 6.72e+01 angle pdb=" C ASP C 48 " pdb=" N PRO C 49 " pdb=" CA PRO C 49 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.39e+01 angle pdb=" CA HIS A 206 " pdb=" CB HIS A 206 " pdb=" CG HIS A 206 " ideal model delta sigma weight residual 113.80 121.66 -7.86 1.00e+00 1.00e+00 6.17e+01 ... (remaining 10994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4669 17.89 - 35.78: 125 35.78 - 53.67: 27 53.67 - 71.56: 11 71.56 - 89.45: 5 Dihedral angle restraints: 4837 sinusoidal: 1925 harmonic: 2912 Sorted by residual: dihedral pdb=" C TRP B 82 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " ideal model delta harmonic sigma weight residual -122.60 -112.93 -9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS A 206 " pdb=" N HIS A 206 " pdb=" CA HIS A 206 " pdb=" CB HIS A 206 " ideal model delta harmonic sigma weight residual -122.60 -132.24 9.64 0 2.50e+00 1.60e-01 1.49e+01 dihedral pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " pdb=" OD1 ASP N 106 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 4834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 768 0.087 - 0.173: 350 0.173 - 0.259: 83 0.259 - 0.346: 24 0.346 - 0.432: 6 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA TYR R 244 " pdb=" N TYR R 244 " pdb=" C TYR R 244 " pdb=" CB TYR R 244 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CB VAL A 353 " pdb=" CA VAL A 353 " pdb=" CG1 VAL A 353 " pdb=" CG2 VAL A 353 " both_signs ideal model delta sigma weight residual False -2.63 -3.04 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TRP R 337 " pdb=" N TRP R 337 " pdb=" C TRP R 337 " pdb=" CB TRP R 337 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 1228 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 40 " 0.057 2.00e-02 2.50e+03 3.39e-02 2.29e+01 pdb=" CG TYR C 40 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 40 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 40 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 40 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 40 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR C 40 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 40 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.061 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP B 99 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.058 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP B 63 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.030 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2854 2.85 - 3.36: 7983 3.36 - 3.87: 14243 3.87 - 4.39: 17710 4.39 - 4.90: 27899 Nonbonded interactions: 70689 Sorted by model distance: nonbonded pdb=" N ASP R 356 " pdb=" OD1 ASP R 356 " model vdw 2.334 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.369 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.373 3.120 nonbonded pdb=" N ASP R 204 " pdb=" OD1 ASP R 204 " model vdw 2.381 3.120 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.386 3.040 ... (remaining 70684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.630 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.910 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.025 0.183 8123 Z= 1.318 Angle : 1.810 13.022 11007 Z= 1.238 Chirality : 0.105 0.432 1231 Planarity : 0.010 0.123 1404 Dihedral : 10.263 89.446 2937 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 982 helix: 0.01 (0.23), residues: 388 sheet: 1.19 (0.34), residues: 198 loop : 0.47 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 27 TYR 0.059 0.008 TYR C 40 PHE 0.037 0.007 PHE R 164 TRP 0.061 0.011 TRP B 99 HIS 0.016 0.004 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.02482 ( 8119) covalent geometry : angle 1.80725 (10999) SS BOND : bond 0.00614 ( 4) SS BOND : angle 4.23785 ( 8) hydrogen bonds : bond 0.14470 ( 428) hydrogen bonds : angle 7.06771 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.7197 (p0) cc_final: 0.6997 (p0) REVERT: R 324 LYS cc_start: 0.8015 (tttt) cc_final: 0.7691 (ttmm) REVERT: R 355 PRO cc_start: 0.8131 (Cg_exo) cc_final: 0.7918 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1183 time to fit residues: 40.2273 Evaluate side-chains 164 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 206 HIS A 253 GLN A 373 HIS N 120 GLN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** 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 = 0.3805 r_free = 0.3805 target = 0.128158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107896 restraints weight = 13337.085| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.54 r_work: 0.3417 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8123 Z= 0.204 Angle : 0.701 8.567 11007 Z= 0.383 Chirality : 0.047 0.342 1231 Planarity : 0.005 0.043 1404 Dihedral : 5.957 42.427 1106 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.99 % Allowed : 10.30 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 982 helix: 1.07 (0.25), residues: 397 sheet: 0.48 (0.33), residues: 187 loop : 0.08 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.029 0.002 TYR N 60 PHE 0.026 0.002 PHE N 68 TRP 0.024 0.002 TRP B 99 HIS 0.009 0.002 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8119) covalent geometry : angle 0.69934 (10999) SS BOND : bond 0.00277 ( 4) SS BOND : angle 2.03566 ( 8) hydrogen bonds : bond 0.05209 ( 428) hydrogen bonds : angle 5.43360 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASN cc_start: 0.9123 (m-40) cc_final: 0.8904 (m110) REVERT: A 358 ILE cc_start: 0.9172 (tt) cc_final: 0.8878 (tp) REVERT: B 13 GLN cc_start: 0.8779 (tt0) cc_final: 0.8417 (pt0) REVERT: B 111 TYR cc_start: 0.8747 (m-80) cc_final: 0.8420 (m-80) REVERT: B 130 GLU cc_start: 0.7174 (pt0) cc_final: 0.6943 (pt0) REVERT: B 134 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7559 (ptm160) REVERT: B 172 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8100 (mp0) REVERT: B 291 ASP cc_start: 0.7451 (t70) cc_final: 0.7229 (t70) REVERT: B 339 TRP cc_start: 0.8851 (m100) cc_final: 0.8366 (m-10) REVERT: C 58 GLU cc_start: 0.7978 (mp0) cc_final: 0.7639 (mp0) REVERT: N 95 TYR cc_start: 0.8669 (m-80) cc_final: 0.8283 (m-80) REVERT: N 105 ARG cc_start: 0.8358 (mtp180) cc_final: 0.8116 (mtp-110) REVERT: R 110 LEU cc_start: 0.7944 (mp) cc_final: 0.6963 (tt) REVERT: R 324 LYS cc_start: 0.7301 (tttt) cc_final: 0.6977 (ttmm) REVERT: R 328 ILE cc_start: 0.8629 (mt) cc_final: 0.8378 (tt) REVERT: R 335 LEU cc_start: 0.7952 (tp) cc_final: 0.7436 (mp) outliers start: 17 outliers final: 12 residues processed: 208 average time/residue: 0.0999 time to fit residues: 27.2772 Evaluate side-chains 181 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 206 HIS A 253 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 94 ASN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** 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 = 0.3790 r_free = 0.3790 target = 0.126875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106687 restraints weight = 13268.607| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.52 r_work: 0.3375 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8123 Z= 0.176 Angle : 0.625 6.494 11007 Z= 0.335 Chirality : 0.045 0.299 1231 Planarity : 0.004 0.045 1404 Dihedral : 5.756 46.258 1106 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.16 % Allowed : 12.65 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 982 helix: 1.05 (0.25), residues: 404 sheet: -0.04 (0.33), residues: 196 loop : 0.22 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.026 0.002 TYR N 60 PHE 0.024 0.002 PHE N 68 TRP 0.022 0.002 TRP R 199 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8119) covalent geometry : angle 0.62289 (10999) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.78795 ( 8) hydrogen bonds : bond 0.04428 ( 428) hydrogen bonds : angle 5.15118 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.9182 (tt) cc_final: 0.8940 (tp) REVERT: B 6 GLN cc_start: 0.8934 (mt0) cc_final: 0.8460 (mp10) REVERT: B 59 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: B 111 TYR cc_start: 0.8784 (m-80) cc_final: 0.8535 (m-80) REVERT: B 118 ASP cc_start: 0.8093 (m-30) cc_final: 0.7669 (m-30) REVERT: B 134 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7570 (ptm160) REVERT: B 334 SER cc_start: 0.9106 (m) cc_final: 0.8877 (m) REVERT: C 42 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8087 (mm-30) REVERT: C 58 GLU cc_start: 0.8007 (mp0) cc_final: 0.7721 (mp0) REVERT: N 95 TYR cc_start: 0.8642 (m-80) cc_final: 0.8377 (m-80) REVERT: R 110 LEU cc_start: 0.7902 (mp) cc_final: 0.6938 (tt) REVERT: R 320 GLN cc_start: 0.5023 (mt0) cc_final: 0.4807 (pt0) REVERT: R 324 LYS cc_start: 0.7174 (tttt) cc_final: 0.6732 (ttmm) REVERT: R 335 LEU cc_start: 0.7992 (tp) cc_final: 0.7590 (mp) REVERT: R 351 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7431 (ttm-80) outliers start: 27 outliers final: 16 residues processed: 207 average time/residue: 0.0783 time to fit residues: 21.7055 Evaluate side-chains 186 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 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 253 GLN A 264 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 24 ASN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.124698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104326 restraints weight = 13480.009| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.61 r_work: 0.3330 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8123 Z= 0.183 Angle : 0.641 9.873 11007 Z= 0.341 Chirality : 0.044 0.235 1231 Planarity : 0.004 0.044 1404 Dihedral : 5.758 53.632 1106 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.98 % Allowed : 13.93 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 982 helix: 1.31 (0.26), residues: 397 sheet: -0.15 (0.34), residues: 201 loop : 0.21 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.027 0.002 TYR N 80 PHE 0.019 0.002 PHE N 68 TRP 0.024 0.002 TRP R 199 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8119) covalent geometry : angle 0.63192 (10999) SS BOND : bond 0.00291 ( 4) SS BOND : angle 3.97046 ( 8) hydrogen bonds : bond 0.04178 ( 428) hydrogen bonds : angle 5.07873 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8923 (tp) REVERT: B 6 GLN cc_start: 0.8972 (mt0) cc_final: 0.8721 (mp10) REVERT: B 9 GLN cc_start: 0.8524 (tp40) cc_final: 0.8023 (tp40) REVERT: B 59 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: B 118 ASP cc_start: 0.8119 (m-30) cc_final: 0.7860 (m-30) REVERT: B 130 GLU cc_start: 0.7233 (pt0) cc_final: 0.6938 (pt0) REVERT: B 134 ARG cc_start: 0.7803 (ptp-170) cc_final: 0.7381 (ptm-80) REVERT: B 334 SER cc_start: 0.9062 (m) cc_final: 0.8834 (m) REVERT: C 22 GLU cc_start: 0.8206 (tp30) cc_final: 0.7809 (tp30) REVERT: C 42 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8206 (mm-30) REVERT: C 58 GLU cc_start: 0.8029 (mp0) cc_final: 0.7377 (mp0) REVERT: R 110 LEU cc_start: 0.7924 (mp) cc_final: 0.7009 (tt) REVERT: R 324 LYS cc_start: 0.7058 (tttt) cc_final: 0.6588 (ttmm) REVERT: R 335 LEU cc_start: 0.7979 (tp) cc_final: 0.7506 (mp) outliers start: 34 outliers final: 20 residues processed: 200 average time/residue: 0.0790 time to fit residues: 21.2324 Evaluate side-chains 189 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 67.7014 > 50: distance: 123 - 127: 12.450 distance: 126 - 188: 21.529 distance: 127 - 128: 4.159 distance: 127 - 133: 12.454 distance: 128 - 129: 8.860 distance: 128 - 131: 39.864 distance: 129 - 130: 39.872 distance: 129 - 134: 32.374 distance: 131 - 132: 28.474 distance: 132 - 133: 25.380 distance: 134 - 135: 18.231 distance: 135 - 136: 16.478 distance: 135 - 138: 6.559 distance: 136 - 137: 8.450 distance: 136 - 139: 11.565 distance: 139 - 140: 16.811 distance: 139 - 145: 12.300 distance: 140 - 141: 23.114 distance: 140 - 143: 3.160 distance: 141 - 142: 14.284 distance: 141 - 146: 16.773 distance: 143 - 144: 11.843 distance: 144 - 145: 15.781 distance: 146 - 147: 14.063 distance: 147 - 148: 10.864 distance: 147 - 150: 4.107 distance: 148 - 149: 11.180 distance: 148 - 157: 7.498 distance: 150 - 151: 6.640 distance: 151 - 152: 10.303 distance: 151 - 153: 8.377 distance: 152 - 154: 20.157 distance: 153 - 155: 11.789 distance: 154 - 156: 13.532 distance: 155 - 156: 12.400 distance: 157 - 158: 7.987 distance: 158 - 159: 11.940 distance: 158 - 161: 5.211 distance: 159 - 160: 7.475 distance: 159 - 164: 9.880 distance: 161 - 162: 20.084 distance: 161 - 163: 22.856 distance: 164 - 165: 14.926 distance: 165 - 166: 19.074 distance: 165 - 168: 16.040 distance: 166 - 167: 20.190 distance: 166 - 175: 27.306 distance: 168 - 169: 12.997 distance: 169 - 170: 18.353 distance: 170 - 171: 20.187 distance: 171 - 172: 19.510 distance: 172 - 173: 24.625 distance: 172 - 174: 7.274 distance: 175 - 176: 9.345 distance: 176 - 177: 19.912 distance: 176 - 179: 14.419 distance: 177 - 178: 15.348 distance: 177 - 183: 14.373 distance: 179 - 180: 7.801 distance: 180 - 181: 13.807 distance: 180 - 182: 17.357 distance: 183 - 184: 8.834 distance: 184 - 185: 7.456 distance: 184 - 187: 17.717 distance: 185 - 186: 26.102 distance: 185 - 189: 6.360 distance: 187 - 188: 29.851 distance: 189 - 190: 16.245 distance: 190 - 191: 15.390 distance: 191 - 192: 6.171 distance: 191 - 200: 15.783 distance: 193 - 194: 15.514 distance: 194 - 195: 10.315 distance: 194 - 196: 7.205 distance: 195 - 197: 3.837 distance: 196 - 198: 8.312 distance: 197 - 199: 6.178 distance: 198 - 199: 6.029 distance: 200 - 201: 5.622 distance: 201 - 202: 5.109 distance: 201 - 204: 5.328 distance: 202 - 203: 10.375 distance: 202 - 208: 8.205 distance: 204 - 205: 6.680 distance: 205 - 206: 12.053 distance: 205 - 207: 9.375