Starting phenix.real_space_refine on Fri Aug 22 12:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e0f_30931/08_2025/7e0f_30931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e0f_30931/08_2025/7e0f_30931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e0f_30931/08_2025/7e0f_30931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e0f_30931/08_2025/7e0f_30931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e0f_30931/08_2025/7e0f_30931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e0f_30931/08_2025/7e0f_30931.map" } resolution = 3.02 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1248 2.51 5 N 354 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 2022 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.57, per 1000 atoms: 0.28 Number of scatterers: 2022 At special positions: 0 Unit cell: (79.5, 81.62, 34.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 354 7.00 C 1248 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: 0.29 Conformation dependent library (CDL) restraints added in 167.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.582A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.344A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.385A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 93 through 94 16 hydrogen bonds defined for protein. 48 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: 0.24 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 378 1.27 - 1.34: 312 1.34 - 1.41: 60 1.41 - 1.47: 366 1.47 - 1.54: 912 Bond restraints: 2028 Sorted by residual: bond pdb=" C GLN C 79 " pdb=" N LYS C 80 " ideal model delta sigma weight residual 1.332 1.269 0.064 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C GLN F 79 " pdb=" N LYS F 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" C GLN D 79 " pdb=" N LYS D 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" C GLN B 79 " pdb=" N LYS B 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" C GLN A 79 " pdb=" N LYS A 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.00e+01 ... (remaining 2023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 2321 1.14 - 2.28: 337 2.28 - 3.43: 42 3.43 - 4.57: 42 4.57 - 5.71: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta sigma weight residual 121.58 115.88 5.70 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 angle pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1086 17.15 - 34.29: 84 34.29 - 51.43: 12 51.43 - 68.58: 0 68.58 - 85.72: 12 Dihedral angle restraints: 1194 sinusoidal: 390 harmonic: 804 Sorted by residual: dihedral pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta harmonic sigma weight residual 180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 1191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 161 0.043 - 0.085: 128 0.085 - 0.127: 54 0.127 - 0.169: 17 0.169 - 0.211: 6 Chirality restraints: 366 Sorted by residual: chirality pdb=" CB VAL A 95 " pdb=" CA VAL A 95 " pdb=" CG1 VAL A 95 " pdb=" CG2 VAL A 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 95 " pdb=" CA VAL B 95 " pdb=" CG1 VAL B 95 " pdb=" CG2 VAL B 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 363 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ALA A 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA A 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 90 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA D 90 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA D 90 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 91 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA C 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA C 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA C 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 770 2.85 - 3.36: 1787 3.36 - 3.88: 2984 3.88 - 4.39: 3268 4.39 - 4.90: 6828 Nonbonded interactions: 15637 Sorted by model distance: nonbonded pdb=" OG1 THR D 54 " pdb=" OG1 THR D 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR E 54 " pdb=" OG1 THR E 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR F 54 " pdb=" OG1 THR F 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR B 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR A 64 " model vdw 2.341 3.040 ... (remaining 15632 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.900 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: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.016 0.086 2028 Z= 0.747 Angle : 0.986 5.709 2748 Z= 0.581 Chirality : 0.069 0.211 366 Planarity : 0.003 0.015 348 Dihedral : 15.885 85.718 678 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % 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: -5.10 (0.40), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.007 PHE B 94 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.01578 ( 2028) covalent geometry : angle 0.98648 ( 2748) hydrogen bonds : bond 0.29842 ( 16) hydrogen bonds : angle 11.70191 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.080 Fit side-chains REVERT: B 62 GLN cc_start: 0.8853 (pt0) cc_final: 0.8407 (pt0) REVERT: C 62 GLN cc_start: 0.8813 (pt0) cc_final: 0.8532 (pt0) REVERT: C 83 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7340 (pm20) REVERT: E 60 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7419 (mtpt) REVERT: E 62 GLN cc_start: 0.9017 (pt0) cc_final: 0.8721 (pt0) REVERT: F 61 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8047 (mt-10) REVERT: F 62 GLN cc_start: 0.8878 (pt0) cc_final: 0.8589 (pt0) REVERT: F 83 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7547 (pm20) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0894 time to fit residues: 4.1193 Evaluate side-chains 22 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.205296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.148360 restraints weight = 1991.252| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.04 r_work: 0.4130 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2028 Z= 0.138 Angle : 0.600 4.688 2748 Z= 0.336 Chirality : 0.052 0.127 366 Planarity : 0.002 0.009 348 Dihedral : 5.483 25.243 288 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.39 % Allowed : 15.20 % Favored : 79.41 % 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: -4.51 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE B 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2028) covalent geometry : angle 0.60019 ( 2748) hydrogen bonds : bond 0.04894 ( 16) hydrogen bonds : angle 6.98584 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.076 Fit side-chains REVERT: B 62 GLN cc_start: 0.8654 (pt0) cc_final: 0.8428 (pt0) REVERT: C 61 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 83 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7340 (pm20) REVERT: E 62 GLN cc_start: 0.8814 (pt0) cc_final: 0.8438 (pt0) REVERT: F 61 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8013 (mt-10) REVERT: F 83 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7513 (pm20) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.0456 time to fit residues: 2.7560 Evaluate side-chains 37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5643 > 50: distance: 38 - 137: 6.582 distance: 52 - 140: 16.815 distance: 108 - 112: 8.183 distance: 112 - 113: 19.450 distance: 113 - 114: 12.312 distance: 113 - 116: 18.667 distance: 114 - 115: 32.227 distance: 114 - 119: 15.128 distance: 116 - 117: 21.113 distance: 116 - 118: 19.278 distance: 119 - 120: 26.137 distance: 120 - 121: 24.248 distance: 120 - 123: 19.509 distance: 121 - 122: 25.877 distance: 121 - 128: 14.532 distance: 123 - 124: 10.076 distance: 124 - 125: 15.814 distance: 125 - 126: 7.935 distance: 126 - 127: 5.587 distance: 128 - 129: 6.513 distance: 129 - 130: 5.956 distance: 129 - 132: 9.357 distance: 130 - 131: 15.641 distance: 130 - 137: 9.415 distance: 131 - 222: 22.595 distance: 132 - 133: 10.423 distance: 133 - 134: 5.142 distance: 134 - 135: 3.761 distance: 134 - 136: 4.422 distance: 137 - 138: 7.481 distance: 138 - 139: 6.363 distance: 138 - 141: 12.631 distance: 139 - 140: 8.550 distance: 139 - 146: 13.983 distance: 141 - 142: 4.703 distance: 142 - 143: 7.150 distance: 143 - 144: 4.686 distance: 143 - 145: 4.997 distance: 146 - 147: 11.002 distance: 146 - 225: 5.507 distance: 147 - 148: 14.919 distance: 147 - 150: 3.005 distance: 148 - 149: 18.842 distance: 148 - 153: 14.425 distance: 150 - 151: 24.069 distance: 150 - 152: 11.720 distance: 153 - 154: 4.324 distance: 154 - 157: 7.655 distance: 155 - 156: 9.223 distance: 155 - 160: 10.025 distance: 157 - 158: 3.158 distance: 157 - 159: 3.112 distance: 160 - 161: 12.142 distance: 161 - 162: 12.382 distance: 161 - 164: 9.094 distance: 162 - 163: 13.415 distance: 162 - 168: 21.685 distance: 164 - 165: 10.641 distance: 165 - 166: 14.011 distance: 165 - 167: 8.804 distance: 168 - 169: 17.088 distance: 169 - 170: 18.828 distance: 169 - 172: 9.010 distance: 170 - 171: 6.709 distance: 170 - 175: 11.977 distance: 172 - 173: 9.996 distance: 172 - 174: 7.004 distance: 175 - 176: 17.515 distance: 176 - 177: 15.004 distance: 177 - 178: 29.542 distance: 177 - 179: 4.380 distance: 179 - 180: 5.797 distance: 180 - 181: 27.653 distance: 181 - 182: 6.000 distance: 181 - 183: 26.471