Starting phenix.real_space_refine on Fri Aug 22 15:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efp_28087/08_2025/8efp_28087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efp_28087/08_2025/8efp_28087.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/8efp_28087/08_2025/8efp_28087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2025/8efp_28087.map" model { file = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2025/8efp_28087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2025/8efp_28087.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= 0.009 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 13 5.16 5 C 2977 2.51 5 N 808 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 4705 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "C" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2729 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 1.12, per 1000 atoms: 0.24 Number of scatterers: 4705 At special positions: 0 Unit cell: (76.176, 74.52, 113.436, 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 13 16.00 O 907 8.00 N 808 7.00 C 2977 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: 0.33 Conformation dependent library (CDL) restraints added in 208.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 40.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.524A pdb=" N PHE B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'C' and resid 4 through 18 removed outlier: 3.527A pdb=" N ALA C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.179A pdb=" N ASP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.660A pdb=" N ARG C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.258A pdb=" N HIS C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 281 through 299 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 354 through 369 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'C' and resid 383 through 404 Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.594A pdb=" N LEU B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 102 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.521A pdb=" N CYS B 183 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 204 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 230 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR B 206 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.853A pdb=" N SER C 206 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 160 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS C 210 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL C 158 " --> pdb=" O LYS C 210 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 522 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: 0.62 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 959 1.33 - 1.45: 1038 1.45 - 1.57: 2773 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4790 Sorted by residual: bond pdb=" N LEU C 263 " pdb=" CA LEU C 263 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N ASP C 173 " pdb=" CA ASP C 173 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.70e-03 1.06e+04 9.06e+00 bond pdb=" N LYS C 177 " pdb=" CA LYS C 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.26e-02 6.30e+03 8.83e+00 bond pdb=" CA LYS C 177 " pdb=" C LYS C 177 " ideal model delta sigma weight residual 1.519 1.534 -0.016 5.30e-03 3.56e+04 8.82e+00 bond pdb=" N THR C 264 " pdb=" CA THR C 264 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.33e-02 5.65e+03 8.68e+00 ... (remaining 4785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 6360 4.02 - 8.05: 109 8.05 - 12.07: 15 12.07 - 16.09: 5 16.09 - 20.12: 6 Bond angle restraints: 6495 Sorted by residual: angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 113.37 93.25 20.12 1.61e+00 3.86e-01 1.56e+02 angle pdb=" N SER C 180 " pdb=" CA SER C 180 " pdb=" C SER C 180 " ideal model delta sigma weight residual 112.94 95.36 17.58 1.41e+00 5.03e-01 1.56e+02 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 111.19 94.15 17.04 1.57e+00 4.06e-01 1.18e+02 angle pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" C GLN C 194 " ideal model delta sigma weight residual 108.23 89.70 18.53 1.72e+00 3.38e-01 1.16e+02 angle pdb=" N ARG C 195 " pdb=" CA ARG C 195 " pdb=" C ARG C 195 " ideal model delta sigma weight residual 108.76 93.60 15.16 1.69e+00 3.50e-01 8.05e+01 ... (remaining 6490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 2474 18.18 - 36.37: 360 36.37 - 54.55: 101 54.55 - 72.73: 11 72.73 - 90.91: 8 Dihedral angle restraints: 2954 sinusoidal: 1197 harmonic: 1757 Sorted by residual: dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -97.68 -24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" C VAL C 213 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" CB VAL C 213 " ideal model delta harmonic sigma weight residual -122.00 -103.01 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C GLN C 194 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" CB GLN C 194 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 709 0.147 - 0.293: 30 0.293 - 0.440: 3 0.440 - 0.586: 0 0.586 - 0.733: 5 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA VAL C 213 " pdb=" N VAL C 213 " pdb=" C VAL C 213 " pdb=" CB VAL C 213 " both_signs ideal model delta sigma weight residual False 2.44 3.17 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA TYR C 176 " pdb=" N TYR C 176 " pdb=" C TYR C 176 " pdb=" CB TYR C 176 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP C 179 " pdb=" N TRP C 179 " pdb=" C TRP C 179 " pdb=" CB TRP C 179 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 744 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 95 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 95 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 95 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 96 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 37 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN B 37 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 398 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE C 398 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 398 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 399 " -0.013 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 64 2.51 - 3.10: 3894 3.10 - 3.70: 7797 3.70 - 4.30: 10845 4.30 - 4.90: 16554 Nonbonded interactions: 39154 Sorted by model distance: nonbonded pdb=" O TRP C 179 " pdb=" CG TRP C 179 " model vdw 1.908 3.260 nonbonded pdb=" O TRP C 179 " pdb=" CD2 TRP C 179 " model vdw 2.113 3.260 nonbonded pdb=" N VAL C 213 " pdb=" O VAL C 213 " model vdw 2.191 2.496 nonbonded pdb=" OG1 THR C 151 " pdb=" NH1 ARG C 152 " model vdw 2.219 3.120 nonbonded pdb=" O LYS C 359 " pdb=" N VAL C 362 " model vdw 2.258 3.120 ... (remaining 39149 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 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: 1.050 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.110 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 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 : 0.006 0.052 4790 Z= 0.370 Angle : 1.460 20.115 6495 Z= 0.886 Chirality : 0.085 0.733 747 Planarity : 0.007 0.067 848 Dihedral : 18.607 90.911 1804 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 3.07 % Allowed : 31.03 % Favored : 65.90 % Cbeta Deviations : 1.22 % 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: -4.26 (0.29), residues: 586 helix: -2.31 (0.31), residues: 203 sheet: -3.30 (0.61), residues: 49 loop : -3.21 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 124 TYR 0.027 0.002 TYR C 129 PHE 0.021 0.003 PHE B 98 TRP 0.006 0.002 TRP B 34 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00590 ( 4790) covalent geometry : angle 1.46016 ( 6495) hydrogen bonds : bond 0.14811 ( 177) hydrogen bonds : angle 8.13377 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 TYR cc_start: 0.7911 (m-10) cc_final: 0.7477 (m-10) REVERT: C 275 LEU cc_start: 0.8243 (pp) cc_final: 0.7875 (pp) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.0754 time to fit residues: 7.3899 Evaluate side-chains 50 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 56 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 186 HIS ** C 343 GLN ** 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 = 0.4308 r_free = 0.4308 target = 0.083091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.065210 restraints weight = 29321.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.066587 restraints weight = 20482.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.067654 restraints weight = 15800.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.068234 restraints weight = 12984.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.068912 restraints weight = 11341.143| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4790 Z= 0.192 Angle : 0.889 11.582 6495 Z= 0.447 Chirality : 0.046 0.154 747 Planarity : 0.006 0.067 848 Dihedral : 7.611 59.549 647 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 3.26 % Allowed : 29.69 % Favored : 67.05 % 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: -3.89 (0.30), residues: 586 helix: -1.86 (0.31), residues: 212 sheet: -3.47 (0.56), residues: 54 loop : -3.02 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.018 0.001 TYR B 27 PHE 0.017 0.002 PHE C 34 TRP 0.022 0.004 TRP C 179 HIS 0.004 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4790) covalent geometry : angle 0.88937 ( 6495) hydrogen bonds : bond 0.07232 ( 177) hydrogen bonds : angle 6.80104 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8552 (pp) cc_final: 0.8050 (mt) REVERT: B 108 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5232 (pmt-80) REVERT: C 122 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: C 275 LEU cc_start: 0.8534 (pp) cc_final: 0.8285 (pp) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.0680 time to fit residues: 5.8538 Evaluate side-chains 58 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 87 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.082504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.064523 restraints weight = 29466.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.065921 restraints weight = 20417.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.066976 restraints weight = 15635.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.067760 restraints weight = 12782.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.068269 restraints weight = 10935.088| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4790 Z= 0.165 Angle : 0.813 12.603 6495 Z= 0.402 Chirality : 0.044 0.159 747 Planarity : 0.005 0.064 848 Dihedral : 6.939 55.980 645 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 4.02 % Allowed : 28.35 % Favored : 67.62 % 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: -3.56 (0.31), residues: 586 helix: -1.52 (0.31), residues: 224 sheet: -3.34 (0.55), residues: 56 loop : -2.88 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.013 0.001 TYR B 27 PHE 0.012 0.002 PHE B 192 TRP 0.014 0.002 TRP B 34 HIS 0.007 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4790) covalent geometry : angle 0.81349 ( 6495) hydrogen bonds : bond 0.06279 ( 177) hydrogen bonds : angle 6.14888 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8818 (pp) cc_final: 0.8275 (mt) REVERT: B 108 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5320 (pmt-80) REVERT: C 15 GLU cc_start: 0.9021 (tp30) cc_final: 0.8035 (mp0) REVERT: C 62 LEU cc_start: 0.9441 (tt) cc_final: 0.9215 (mm) REVERT: C 216 ASN cc_start: 0.8746 (m-40) cc_final: 0.8084 (t0) outliers start: 21 outliers final: 8 residues processed: 67 average time/residue: 0.0636 time to fit residues: 5.6098 Evaluate side-chains 53 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.080172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.061965 restraints weight = 27468.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.063359 restraints weight = 18996.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.064459 restraints weight = 14553.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.065259 restraints weight = 11804.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.065810 restraints weight = 10083.798| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4790 Z= 0.176 Angle : 0.812 13.888 6495 Z= 0.397 Chirality : 0.043 0.127 747 Planarity : 0.005 0.061 848 Dihedral : 6.771 54.469 645 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 2.49 % Allowed : 28.16 % Favored : 69.35 % 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: -3.34 (0.32), residues: 586 helix: -1.25 (0.32), residues: 220 sheet: -3.28 (0.50), residues: 72 loop : -2.71 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 285 TYR 0.014 0.001 TYR C 393 PHE 0.010 0.002 PHE B 192 TRP 0.011 0.002 TRP B 34 HIS 0.005 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4790) covalent geometry : angle 0.81181 ( 6495) hydrogen bonds : bond 0.05818 ( 177) hydrogen bonds : angle 6.25701 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.8998 (pt0) cc_final: 0.8644 (pt0) REVERT: B 75 LEU cc_start: 0.8799 (pp) cc_final: 0.8422 (mt) REVERT: B 108 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5310 (pmt-80) REVERT: C 15 GLU cc_start: 0.9059 (tp30) cc_final: 0.8079 (mp0) REVERT: C 62 LEU cc_start: 0.9371 (tt) cc_final: 0.9125 (mm) REVERT: C 147 ARG cc_start: 0.9192 (ptp-170) cc_final: 0.8940 (ptp-170) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.0557 time to fit residues: 4.5972 Evaluate side-chains 58 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.082763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.064705 restraints weight = 29232.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.066177 restraints weight = 20159.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.067232 restraints weight = 15427.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.067985 restraints weight = 12598.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.068549 restraints weight = 10819.302| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4790 Z= 0.146 Angle : 0.782 15.173 6495 Z= 0.379 Chirality : 0.042 0.123 747 Planarity : 0.004 0.056 848 Dihedral : 6.090 28.889 643 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.07 % Allowed : 27.97 % Favored : 68.97 % 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: -3.07 (0.32), residues: 586 helix: -1.07 (0.32), residues: 224 sheet: -3.00 (0.55), residues: 66 loop : -2.59 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.013 0.001 TYR C 393 PHE 0.015 0.002 PHE C 84 TRP 0.012 0.002 TRP B 34 HIS 0.006 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4790) covalent geometry : angle 0.78151 ( 6495) hydrogen bonds : bond 0.05469 ( 177) hydrogen bonds : angle 5.81795 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8816 (pp) cc_final: 0.8480 (mt) REVERT: B 108 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5177 (pmt-80) REVERT: B 163 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6827 (t-90) REVERT: C 15 GLU cc_start: 0.9019 (tp30) cc_final: 0.8036 (mp0) REVERT: C 16 MET cc_start: 0.8620 (tpp) cc_final: 0.7960 (tpp) REVERT: C 62 LEU cc_start: 0.9386 (tt) cc_final: 0.9152 (mm) REVERT: C 84 PHE cc_start: 0.7741 (m-80) cc_final: 0.7180 (m-80) REVERT: C 147 ARG cc_start: 0.9230 (ptp-170) cc_final: 0.9007 (ptp-170) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.0580 time to fit residues: 4.9328 Evaluate side-chains 57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 54.3563 > 50: distance: 70 - 90: 22.780 distance: 74 - 95: 15.187 distance: 80 - 103: 6.356 distance: 84 - 90: 20.306 distance: 85 - 111: 15.524 distance: 90 - 91: 11.546 distance: 91 - 92: 29.787 distance: 91 - 94: 20.236 distance: 92 - 93: 10.603 distance: 92 - 95: 25.106 distance: 93 - 120: 11.695 distance: 95 - 96: 12.171 distance: 96 - 97: 7.538 distance: 96 - 99: 3.353 distance: 97 - 98: 7.625 distance: 97 - 103: 13.974 distance: 99 - 100: 6.570 distance: 100 - 101: 25.932 distance: 100 - 102: 23.756 distance: 103 - 104: 8.372 distance: 104 - 105: 5.818 distance: 104 - 107: 17.224 distance: 105 - 106: 18.853 distance: 105 - 111: 15.503 distance: 107 - 108: 19.622 distance: 108 - 109: 15.980 distance: 108 - 110: 18.995 distance: 112 - 113: 16.475 distance: 112 - 115: 20.677 distance: 113 - 114: 22.283 distance: 113 - 120: 7.924 distance: 115 - 116: 17.712 distance: 116 - 117: 37.931 distance: 117 - 118: 5.824 distance: 117 - 119: 15.292 distance: 120 - 121: 24.691 distance: 121 - 122: 10.121 distance: 121 - 124: 22.307 distance: 124 - 125: 34.677 distance: 125 - 126: 17.677 distance: 125 - 127: 29.333 distance: 129 - 130: 15.936 distance: 129 - 132: 32.087 distance: 130 - 131: 25.569 distance: 130 - 134: 23.606 distance: 132 - 133: 14.244 distance: 135 - 136: 17.376 distance: 135 - 138: 3.937 distance: 136 - 143: 18.221 distance: 138 - 139: 5.976 distance: 139 - 140: 21.061 distance: 140 - 141: 9.396 distance: 140 - 142: 21.905 distance: 143 - 144: 19.945 distance: 144 - 145: 53.041 distance: 144 - 147: 18.723 distance: 145 - 146: 19.811 distance: 145 - 152: 54.356 distance: 146 - 180: 24.500 distance: 147 - 148: 21.329 distance: 148 - 149: 19.974 distance: 149 - 150: 23.424 distance: 149 - 151: 12.690 distance: 152 - 153: 13.171 distance: 153 - 154: 14.286 distance: 153 - 156: 6.985 distance: 154 - 155: 6.319 distance: 154 - 161: 5.546 distance: 155 - 186: 20.114 distance: 156 - 157: 18.814 distance: 157 - 158: 3.823 distance: 158 - 159: 12.999 distance: 158 - 160: 28.398 distance: 161 - 162: 10.004 distance: 162 - 163: 8.026 distance: 162 - 165: 9.691 distance: 163 - 164: 12.648 distance: 163 - 170: 12.961 distance: 164 - 191: 15.166 distance: 165 - 166: 9.039 distance: 166 - 167: 31.666 distance: 167 - 168: 5.241 distance: 167 - 169: 8.757