Starting phenix.real_space_refine on Fri Aug 22 16:42:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrx_34981/08_2025/8hrx_34981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrx_34981/08_2025/8hrx_34981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2025/8hrx_34981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2025/8hrx_34981.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2025/8hrx_34981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2025/8hrx_34981.cif" } resolution = 2.89 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 43 5.16 5 C 3872 2.51 5 N 973 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s 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: 6013 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2322 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 7, 'TRANS': 39} Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1661 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "L" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1659 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Time building chain proxies: 1.40, per 1000 atoms: 0.23 Number of scatterers: 6013 At special positions: 0 Unit cell: (74.7, 68.06, 144.42, 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 43 16.00 O 1125 8.00 N 973 7.00 C 3872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 0.42 Conformation dependent library (CDL) restraints added in 174.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 34.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 84 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.906A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 Proline residue: A 135 - end of helix removed outlier: 3.891A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.603A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.604A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.150A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.638A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 311 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.618A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.601A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 125 through 129 removed outlier: 4.074A pdb=" N LEU H 129 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 125 through 129 removed outlier: 4.074A pdb=" N LEU H 129 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 156 through 158 removed outlier: 3.667A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.729A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS L 39 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.726A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.726A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.540A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA L 196 " --> pdb=" O ILE L 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 205 " --> pdb=" O ALA L 196 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 846 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: 0.77 Time building geometry restraints manager: 0.55 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: 1804 1.34 - 1.46: 1151 1.46 - 1.58: 3145 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 6165 Sorted by residual: bond pdb=" CA SER H 21 " pdb=" C SER H 21 " ideal model delta sigma weight residual 1.522 1.550 -0.027 1.19e-02 7.06e+03 5.21e+00 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" CA MET H 20 " pdb=" C MET H 20 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.20e-02 6.94e+03 3.66e+00 bond pdb=" CA LYS H 19 " pdb=" C LYS H 19 " ideal model delta sigma weight residual 1.521 1.543 -0.022 1.24e-02 6.50e+03 3.20e+00 bond pdb=" C SER L 208 " pdb=" O SER L 208 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.21e-02 6.83e+03 2.77e+00 ... (remaining 6160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 8244 2.39 - 4.79: 118 4.79 - 7.18: 18 7.18 - 9.57: 4 9.57 - 11.96: 2 Bond angle restraints: 8386 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.72 116.90 -6.18 1.01e+00 9.80e-01 3.74e+01 angle pdb=" N LYS L 207 " pdb=" CA LYS L 207 " pdb=" C LYS L 207 " ideal model delta sigma weight residual 108.76 99.12 9.64 1.69e+00 3.50e-01 3.25e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 115.29 -4.67 1.02e+00 9.61e-01 2.10e+01 angle pdb=" N ALA A 217 " pdb=" CA ALA A 217 " pdb=" C ALA A 217 " ideal model delta sigma weight residual 113.16 118.52 -5.36 1.24e+00 6.50e-01 1.87e+01 angle pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" C PHE A 216 " ideal model delta sigma weight residual 111.36 116.02 -4.66 1.09e+00 8.42e-01 1.83e+01 ... (remaining 8381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3131 17.51 - 35.03: 403 35.03 - 52.54: 111 52.54 - 70.06: 13 70.06 - 87.57: 7 Dihedral angle restraints: 3665 sinusoidal: 1412 harmonic: 2253 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -6.91 -79.09 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS H 145 " pdb=" SG CYS H 145 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 38.53 54.47 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA ALA H 92 " pdb=" C ALA H 92 " pdb=" N VAL H 93 " pdb=" CA VAL H 93 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 805 0.059 - 0.118: 140 0.118 - 0.176: 12 0.176 - 0.235: 1 0.235 - 0.294: 1 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA LYS L 207 " pdb=" N LYS L 207 " pdb=" C LYS L 207 " pdb=" CB LYS L 207 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ALA A 217 " pdb=" N ALA A 217 " pdb=" C ALA A 217 " pdb=" CB ALA A 217 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 956 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 188 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO H 189 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO L 95 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 127 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.06e+00 pdb=" N PRO H 128 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 128 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 128 " 0.020 5.00e-02 4.00e+02 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 12 2.35 - 2.99: 3144 2.99 - 3.62: 8889 3.62 - 4.26: 13333 4.26 - 4.90: 23120 Nonbonded interactions: 48498 Sorted by model distance: nonbonded pdb=" O MET A 218 " pdb=" O THR A 219 " model vdw 1.709 3.040 nonbonded pdb=" CE MET H 20 " pdb=" CE MET H 81 " model vdw 1.734 3.880 nonbonded pdb=" N GLU L 187 " pdb=" OE1 GLU L 187 " model vdw 2.177 3.120 nonbonded pdb=" O GLY H 42 " pdb=" CG LYS H 43 " model vdw 2.212 3.440 nonbonded pdb=" OD1 ASN L 31 " pdb=" OG1 THR L 51 " model vdw 2.269 3.040 ... (remaining 48493 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: 1.530 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.670 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.003 0.043 6169 Z= 0.158 Angle : 0.702 11.963 8394 Z= 0.377 Chirality : 0.045 0.294 959 Planarity : 0.004 0.040 1047 Dihedral : 16.539 87.569 2211 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 3.52 % Allowed : 31.57 % Favored : 64.90 % 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: 0.01 (0.31), residues: 772 helix: 1.63 (0.33), residues: 251 sheet: -0.23 (0.41), residues: 188 loop : -1.11 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 53 TYR 0.014 0.001 TYR L 173 PHE 0.007 0.001 PHE A 285 TRP 0.010 0.001 TRP H 159 HIS 0.001 0.000 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6165) covalent geometry : angle 0.70035 ( 8386) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.49375 ( 8) hydrogen bonds : bond 0.17545 ( 279) hydrogen bonds : angle 7.49067 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.240 Fit side-chains REVERT: L 207 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6888 (mmmm) outliers start: 24 outliers final: 21 residues processed: 170 average time/residue: 0.3386 time to fit residues: 61.8670 Evaluate side-chains 166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 205 ILE 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: 72.0273 > 50: distance: 5 - 107: 3.118 distance: 26 - 31: 35.585 distance: 31 - 32: 38.767 distance: 32 - 35: 56.710 distance: 33 - 34: 40.146 distance: 39 - 40: 38.874 distance: 39 - 42: 57.100 distance: 40 - 41: 41.082 distance: 40 - 49: 39.566 distance: 42 - 43: 38.993 distance: 43 - 44: 40.058 distance: 44 - 46: 39.246 distance: 45 - 47: 56.344 distance: 49 - 50: 40.363 distance: 49 - 55: 39.094 distance: 50 - 51: 57.118 distance: 50 - 53: 58.012 distance: 53 - 54: 40.599 distance: 54 - 55: 40.275 distance: 57 - 60: 56.622 distance: 58 - 59: 40.699 distance: 61 - 62: 40.009 distance: 61 - 119: 36.625 distance: 62 - 65: 39.249 distance: 63 - 69: 39.726 distance: 64 - 116: 35.003 distance: 69 - 70: 70.510 distance: 70 - 73: 57.003 distance: 71 - 77: 40.508 distance: 74 - 76: 57.757 distance: 77 - 78: 39.274 distance: 78 - 79: 41.412 distance: 79 - 80: 39.519 distance: 79 - 86: 39.991 distance: 86 - 87: 38.635 distance: 87 - 88: 40.914 distance: 87 - 90: 57.098 distance: 88 - 92: 56.567 distance: 90 - 91: 39.927 distance: 93 - 94: 40.005 distance: 94 - 96: 56.394 distance: 96 - 97: 6.629 distance: 97 - 98: 8.602 distance: 97 - 100: 6.304 distance: 98 - 104: 33.928 distance: 100 - 101: 69.787 distance: 101 - 102: 55.114 distance: 101 - 103: 41.463