Starting phenix.real_space_refine on Fri Aug 22 19:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qnu_4609/08_2025/6qnu_4609.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qnu_4609/08_2025/6qnu_4609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qnu_4609/08_2025/6qnu_4609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qnu_4609/08_2025/6qnu_4609.map" model { file = "/net/cci-nas-00/data/ceres_data/6qnu_4609/08_2025/6qnu_4609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qnu_4609/08_2025/6qnu_4609.cif" } resolution = 3.8 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= 0.008 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 22 5.16 5 C 4655 2.51 5 N 1169 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 7250 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 2 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1409 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain breaks: 5 Time building chain proxies: 2.06, per 1000 atoms: 0.28 Number of scatterers: 7250 At special positions: 0 Unit cell: (94.963, 105.633, 93.896, 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 22 16.00 O 1404 8.00 N 1169 7.00 C 4655 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: 0.55 Conformation dependent library (CDL) restraints added in 442.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 17 sheets defined 2.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.583A pdb=" N ASN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.153A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.424A pdb=" N GLY E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL A 269 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 196 removed outlier: 3.734A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.175A pdb=" N LEU C 305 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.652A pdb=" N PHE C 312 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 197 removed outlier: 5.542A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.401A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 191 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 151 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG D 193 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR D 149 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.854A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 170 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.722A pdb=" N VAL D 222 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 259 through 263 removed outlier: 3.753A pdb=" N VAL D 303 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 324 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.511A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 190 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.724A pdb=" N ILE E 171 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.521A pdb=" N VAL E 222 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 229 through 232 removed outlier: 6.681A pdb=" N GLY E 230 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB8, first strand: chain 'E' and resid 272 through 277 188 hydrogen bonds defined for protein. 507 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: 1.05 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.46: 1349 1.46 - 1.57: 3752 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 7399 Sorted by residual: bond pdb=" C GLU E 155 " pdb=" N PRO E 156 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 bond pdb=" CA THR A 304 " pdb=" CB THR A 304 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.95e+00 bond pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.64e+00 bond pdb=" CA TYR E 158 " pdb=" C TYR E 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.63e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 9719 2.17 - 4.34: 270 4.34 - 6.51: 39 6.51 - 8.68: 18 8.68 - 10.85: 4 Bond angle restraints: 10050 Sorted by residual: angle pdb=" C ALA A 303 " pdb=" N THR A 304 " pdb=" CA THR A 304 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C ASN D 219 " pdb=" N ILE D 220 " pdb=" CA ILE D 220 " ideal model delta sigma weight residual 122.13 130.06 -7.93 1.85e+00 2.92e-01 1.84e+01 angle pdb=" N ILE D 315 " pdb=" CA ILE D 315 " pdb=" C ILE D 315 " ideal model delta sigma weight residual 113.71 109.68 4.03 9.50e-01 1.11e+00 1.80e+01 angle pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N TRP D 257 " pdb=" CA TRP D 257 " pdb=" C TRP D 257 " ideal model delta sigma weight residual 114.04 109.06 4.98 1.24e+00 6.50e-01 1.62e+01 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3940 16.84 - 33.69: 390 33.69 - 50.53: 66 50.53 - 67.37: 11 67.37 - 84.22: 6 Dihedral angle restraints: 4413 sinusoidal: 1724 harmonic: 2689 Sorted by residual: dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual -180.00 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 dihedral pdb=" CA ASP D 218 " pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 845 0.053 - 0.106: 236 0.106 - 0.159: 77 0.159 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA TYR E 158 " pdb=" N TYR E 158 " pdb=" C TYR E 158 " pdb=" CB TYR E 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR D 158 " pdb=" N TYR D 158 " pdb=" C TYR D 158 " pdb=" CB TYR D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE C 306 " pdb=" CA ILE C 306 " pdb=" CG1 ILE C 306 " pdb=" CG2 ILE C 306 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1167 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C LYS B 275 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 276 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 219 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASN E 219 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN E 219 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE E 220 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 308 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 309 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2300 2.84 - 3.35: 5486 3.35 - 3.87: 11611 3.87 - 4.38: 12135 4.38 - 4.90: 22568 Nonbonded interactions: 54100 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.324 3.040 nonbonded pdb=" OE1 GLU C 194 " pdb=" OH TYR C 196 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR C 135 " pdb=" O LEU C 158 " model vdw 2.349 3.040 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.351 3.040 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.392 3.040 ... (remaining 54095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ ugh 318)) selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318)) } ncs_group { reference = (chain 'D' and (resid 108 through 134 or resid 146 through 193 or resid 206 thro \ ugh 233 or resid 238 through 291 or resid 299 through 331)) selection = chain 'E' } 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 group one per residue 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: 0.570 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.130 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.004 0.045 7399 Z= 0.207 Angle : 0.909 10.852 10050 Z= 0.494 Chirality : 0.057 0.264 1170 Planarity : 0.006 0.054 1269 Dihedral : 13.913 84.215 2671 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.61 % Allowed : 5.89 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.05 (0.24), residues: 880 helix: -4.32 (0.26), residues: 24 sheet: -1.61 (0.27), residues: 323 loop : -3.50 (0.21), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 316 TYR 0.022 0.002 TYR A 170 PHE 0.019 0.002 PHE D 301 TRP 0.014 0.002 TRP A 134 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 7399) covalent geometry : angle 0.90927 (10050) hydrogen bonds : bond 0.12421 ( 176) hydrogen bonds : angle 7.49356 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8376 (mttt) cc_final: 0.8081 (mtpp) REVERT: A 163 ASN cc_start: 0.8567 (t0) cc_final: 0.8292 (t0) REVERT: B 150 GLN cc_start: 0.8680 (mp-120) cc_final: 0.8340 (mt0) REVERT: D 112 GLN cc_start: 0.7803 (mt0) cc_final: 0.7533 (tt0) REVERT: D 164 LEU cc_start: 0.8552 (tp) cc_final: 0.8283 (tp) REVERT: E 208 GLN cc_start: 0.7162 (mt0) cc_final: 0.6729 (mt0) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 0.1229 time to fit residues: 28.5756 Evaluate side-chains 124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 54.5136 > 50: distance: 12 - 207: 4.969 distance: 15 - 204: 4.273 distance: 27 - 192: 3.990 distance: 30 - 189: 6.221 distance: 45 - 173: 9.691 distance: 48 - 170: 7.516 distance: 95 - 200: 11.113 distance: 98 - 197: 4.634 distance: 127 - 132: 5.128 distance: 133 - 134: 4.653 distance: 134 - 135: 8.018 distance: 136 - 137: 6.092 distance: 137 - 138: 6.008 distance: 137 - 139: 5.364 distance: 142 - 143: 7.419 distance: 142 - 146: 4.853 distance: 144 - 145: 11.556 distance: 146 - 147: 4.112 distance: 147 - 148: 7.561 distance: 147 - 150: 6.893 distance: 148 - 149: 6.674 distance: 148 - 157: 7.639 distance: 150 - 151: 5.243 distance: 151 - 152: 5.861 distance: 152 - 153: 6.056 distance: 153 - 154: 9.768 distance: 154 - 155: 19.009 distance: 154 - 156: 11.237 distance: 157 - 158: 13.677 distance: 158 - 159: 15.857 distance: 158 - 161: 14.378 distance: 159 - 160: 19.955 distance: 159 - 164: 24.498 distance: 161 - 162: 31.535 distance: 161 - 163: 31.160 distance: 164 - 165: 7.772 distance: 165 - 166: 22.067 distance: 165 - 168: 13.032 distance: 166 - 167: 14.437 distance: 166 - 170: 8.256 distance: 168 - 169: 11.070 distance: 170 - 171: 4.633 distance: 171 - 172: 4.006 distance: 171 - 174: 6.418 distance: 172 - 173: 7.110 distance: 172 - 182: 5.435 distance: 174 - 175: 3.802 distance: 175 - 176: 7.642 distance: 175 - 177: 8.388 distance: 176 - 178: 6.521 distance: 177 - 179: 6.444 distance: 178 - 180: 8.353 distance: 179 - 180: 6.469 distance: 180 - 181: 7.421 distance: 182 - 183: 3.376 distance: 183 - 184: 3.091 distance: 183 - 186: 3.739 distance: 184 - 185: 4.662 distance: 184 - 189: 3.034 distance: 186 - 187: 8.987 distance: 186 - 188: 5.901 distance: 189 - 190: 3.882 distance: 191 - 192: 5.389 distance: 193 - 194: 7.411 distance: 194 - 195: 9.284 distance: 195 - 196: 7.068 distance: 198 - 199: 5.439 distance: 198 - 201: 7.893 distance: 199 - 200: 6.819 distance: 199 - 204: 6.773 distance: 201 - 202: 12.767 distance: 201 - 203: 13.347 distance: 205 - 208: 4.476 distance: 206 - 207: 3.737 distance: 209 - 210: 7.034 distance: 210 - 212: 3.278 distance: 211 - 213: 4.595 distance: 212 - 214: 3.805 distance: 213 - 214: 3.114