Starting phenix.real_space_refine on Sat May 2 11:58:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqs_45821/05_2026/9cqs_45821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqs_45821/05_2026/9cqs_45821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2026/9cqs_45821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2026/9cqs_45821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2026/9cqs_45821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2026/9cqs_45821.map" } resolution = 2.52 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= 0.023 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 12 5.16 5 C 2914 2.51 5 N 764 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4790 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1050 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1050 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH B 331 " occ=0.78 Time building chain proxies: 1.06, per 1000 atoms: 0.22 Number of scatterers: 4790 At special positions: 0 Unit cell: (77.175, 72.03, 65.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 12 16.00 O 1096 8.00 N 764 7.00 C 2914 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 95.0 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.683A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 4.105A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.985A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.370A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 99 through 119 removed outlier: 4.027A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.597A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 94 through 113 removed outlier: 4.100A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.977A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.092A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 57 through 77 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.550A pdb=" N LYS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.739A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 Processing helix chain 'D' and resid 143 through 146 333 hydrogen bonds defined for protein. 951 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: 0.50 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1627 1.38 - 1.55: 2966 1.55 - 1.72: 11 1.72 - 1.89: 18 1.89 - 2.06: 16 Bond restraints: 4638 Sorted by residual: bond pdb=" O1 OXY D 202 " pdb=" O2 OXY D 202 " ideal model delta sigma weight residual 1.109 1.209 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O1 OXY B 202 " pdb=" O2 OXY B 202 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" O1 OXY A 202 " pdb=" O2 OXY A 202 " ideal model delta sigma weight residual 1.109 1.206 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O1 OXY C 202 " pdb=" O2 OXY C 202 " ideal model delta sigma weight residual 1.109 1.205 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" N VAL B 18 " pdb=" CA VAL B 18 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.27e-02 6.20e+03 9.75e+00 ... (remaining 4633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 6139 1.78 - 3.56: 181 3.56 - 5.34: 32 5.34 - 7.12: 5 7.12 - 8.90: 1 Bond angle restraints: 6358 Sorted by residual: angle pdb=" CA LYS A 16 " pdb=" CB LYS A 16 " pdb=" CG LYS A 16 " ideal model delta sigma weight residual 114.10 123.00 -8.90 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CA LYS B 17 " pdb=" C LYS B 17 " pdb=" O LYS B 17 " ideal model delta sigma weight residual 120.55 116.92 3.63 1.06e+00 8.90e-01 1.17e+01 angle pdb=" CA VAL B 23 " pdb=" C VAL B 23 " pdb=" O VAL B 23 " ideal model delta sigma weight residual 121.17 117.63 3.54 1.06e+00 8.90e-01 1.12e+01 angle pdb=" CA SER C 133 " pdb=" C SER C 133 " pdb=" O SER C 133 " ideal model delta sigma weight residual 120.55 117.05 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" CA GLY B 24 " pdb=" C GLY B 24 " pdb=" O GLY B 24 " ideal model delta sigma weight residual 120.75 117.57 3.18 1.03e+00 9.43e-01 9.53e+00 ... (remaining 6353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2247 17.14 - 34.28: 262 34.28 - 51.43: 90 51.43 - 68.57: 19 68.57 - 85.71: 8 Dihedral angle restraints: 2626 sinusoidal: 998 harmonic: 1628 Sorted by residual: dihedral pdb=" CA LYS C 16 " pdb=" C LYS C 16 " pdb=" N VAL C 17 " pdb=" CA VAL C 17 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" C1A HEM C 201 " pdb=" C2A HEM C 201 " pdb=" CAA HEM C 201 " pdb=" CBA HEM C 201 " ideal model delta sinusoidal sigma weight residual 0.00 85.71 -85.71 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C2D HEM D 201 " pdb=" C3D HEM D 201 " pdb=" CAD HEM D 201 " pdb=" CBD HEM D 201 " ideal model delta sinusoidal sigma weight residual 180.00 100.77 79.23 2 2.00e+01 2.50e-03 1.16e+01 ... (remaining 2623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 616 0.070 - 0.141: 64 0.141 - 0.211: 6 0.211 - 0.281: 1 0.281 - 0.352: 1 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB VAL B 18 " pdb=" CA VAL B 18 " pdb=" CG1 VAL B 18 " pdb=" CG2 VAL B 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA VAL B 18 " pdb=" N VAL B 18 " pdb=" C VAL B 18 " pdb=" CB VAL B 18 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL C 132 " pdb=" N VAL C 132 " pdb=" C VAL C 132 " pdb=" CB VAL C 132 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 685 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 94 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO C 95 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 94 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 95 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 19 " 0.008 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ASN B 19 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN B 19 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 20 " 0.010 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 149 2.66 - 3.22: 4300 3.22 - 3.78: 8370 3.78 - 4.34: 11759 4.34 - 4.90: 18228 Nonbonded interactions: 42806 Sorted by model distance: nonbonded pdb=" O VAL C 93 " pdb=" OH TYR C 140 " model vdw 2.103 3.040 nonbonded pdb=" NE2 HIS D 92 " pdb="FE HEM D 201 " model vdw 2.139 3.080 nonbonded pdb=" NE2 HIS B 92 " pdb="FE HEM B 201 " model vdw 2.145 3.080 nonbonded pdb=" NE2 HIS A 87 " pdb="FE HEM A 201 " model vdw 2.157 3.080 nonbonded pdb=" O HOH A 323 " pdb=" O HOH A 366 " model vdw 2.161 3.040 ... (remaining 42801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.78 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.320 Find NCS groups from input model: 0.070 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:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.014 0.580 4642 Z= 0.294 Angle : 0.710 8.899 6358 Z= 0.414 Chirality : 0.048 0.352 688 Planarity : 0.006 0.051 794 Dihedral : 17.313 85.710 1574 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.88 % Allowed : 17.84 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.37), residues: 560 helix: 2.54 (0.25), residues: 432 sheet: None (None), residues: 0 loop : 1.83 (0.68), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 104 TYR 0.010 0.002 TYR D 35 PHE 0.018 0.002 PHE D 45 TRP 0.016 0.002 TRP B 15 HIS 0.006 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 4638) covalent geometry : angle 0.71011 ( 6358) hydrogen bonds : bond 0.09791 ( 333) hydrogen bonds : angle 4.05617 ( 951) Misc. bond : bond 0.42848 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.125 Fit side-chains REVERT: A 56 LYS cc_start: 0.7646 (mttt) cc_final: 0.6870 (mptt) REVERT: A 76 MET cc_start: 0.7901 (mtt) cc_final: 0.7532 (mtt) REVERT: B 61 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7126 (tttm) REVERT: C 90 LYS cc_start: 0.8264 (mptt) cc_final: 0.7726 (tttt) REVERT: D 120 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7610 (ptmm) outliers start: 4 outliers final: 1 residues processed: 78 average time/residue: 0.5066 time to fit residues: 40.6419 Evaluate side-chains 72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 68 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.145726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118735 restraints weight = 4554.929| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.67 r_work: 0.3182 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.472 4642 Z= 0.135 Angle : 0.713 15.462 6358 Z= 0.263 Chirality : 0.039 0.157 688 Planarity : 0.005 0.051 794 Dihedral : 9.864 86.877 622 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.64 % Allowed : 14.32 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.37), residues: 560 helix: 2.69 (0.25), residues: 432 sheet: None (None), residues: 0 loop : 2.02 (0.67), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.013 0.002 TYR C 24 PHE 0.010 0.001 PHE D 45 TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4638) covalent geometry : angle 0.71349 ( 6358) hydrogen bonds : bond 0.03668 ( 333) hydrogen bonds : angle 3.68205 ( 951) Misc. bond : bond 0.42264 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.097 Fit side-chains REVERT: A 56 LYS cc_start: 0.7474 (mttt) cc_final: 0.6639 (mptt) REVERT: A 92 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7343 (mtp180) REVERT: B 61 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6829 (tttm) REVERT: C 85 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: C 90 LYS cc_start: 0.8293 (mptt) cc_final: 0.7559 (tttt) REVERT: C 116 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7375 (mp0) REVERT: D 90 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7032 (tp30) REVERT: D 120 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7388 (ptmm) outliers start: 12 outliers final: 2 residues processed: 83 average time/residue: 0.5155 time to fit residues: 43.9832 Evaluate side-chains 75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain C residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 58 HIS ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122753 restraints weight = 4822.112| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.33 r_work: 0.3295 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 4642 Z= 0.122 Angle : 0.734 15.753 6358 Z= 0.258 Chirality : 0.039 0.171 688 Planarity : 0.005 0.049 794 Dihedral : 9.691 86.204 620 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.20 % Allowed : 15.64 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.37), residues: 560 helix: 2.68 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 2.06 (0.67), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.014 0.001 TYR C 24 PHE 0.008 0.001 PHE D 45 TRP 0.009 0.001 TRP C 14 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4638) covalent geometry : angle 0.73409 ( 6358) hydrogen bonds : bond 0.03477 ( 333) hydrogen bonds : angle 3.61625 ( 951) Misc. bond : bond 0.09749 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.095 Fit side-chains REVERT: A 56 LYS cc_start: 0.7704 (mttt) cc_final: 0.7147 (mptt) REVERT: A 92 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7547 (mtp180) REVERT: B 61 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7136 (tttm) REVERT: C 85 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: C 90 LYS cc_start: 0.8282 (mptt) cc_final: 0.7721 (tttt) REVERT: C 116 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7686 (mp0) REVERT: D 90 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7293 (tp30) REVERT: D 120 LYS cc_start: 0.8378 (mtpp) cc_final: 0.7681 (ptmm) outliers start: 10 outliers final: 2 residues processed: 75 average time/residue: 0.5304 time to fit residues: 40.8615 Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain C residue 85 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122595 restraints weight = 4800.904| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.33 r_work: 0.3295 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4642 Z= 0.118 Angle : 0.736 16.370 6358 Z= 0.254 Chirality : 0.039 0.171 688 Planarity : 0.005 0.048 794 Dihedral : 9.615 85.884 620 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.64 % Allowed : 16.52 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.82 (0.37), residues: 560 helix: 2.72 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 2.04 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.011 0.001 TYR C 24 PHE 0.008 0.001 PHE D 118 TRP 0.008 0.001 TRP C 14 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4638) covalent geometry : angle 0.73557 ( 6358) hydrogen bonds : bond 0.03343 ( 333) hydrogen bonds : angle 3.56880 ( 951) Misc. bond : bond 0.04662 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.094 Fit side-chains REVERT: A 56 LYS cc_start: 0.7721 (mttt) cc_final: 0.7146 (mptt) REVERT: A 76 MET cc_start: 0.7890 (mtt) cc_final: 0.7533 (mtt) REVERT: A 92 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7566 (mtp180) REVERT: C 85 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: C 90 LYS cc_start: 0.8298 (mptt) cc_final: 0.7747 (tttt) REVERT: D 90 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7249 (tp30) REVERT: D 120 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7671 (ptmm) outliers start: 12 outliers final: 2 residues processed: 77 average time/residue: 0.4382 time to fit residues: 34.7522 Evaluate side-chains 72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4693 > 50: distance: 46 - 51: 28.515 distance: 51 - 52: 47.013 distance: 52 - 53: 42.235 distance: 52 - 55: 8.090 distance: 53 - 54: 6.749 distance: 53 - 59: 29.079 distance: 55 - 56: 23.306 distance: 56 - 57: 44.745 distance: 56 - 58: 17.953 distance: 59 - 60: 16.577 distance: 60 - 61: 9.464 distance: 60 - 63: 13.072 distance: 61 - 62: 38.394 distance: 61 - 70: 13.810 distance: 63 - 64: 17.894 distance: 64 - 65: 24.590 distance: 65 - 66: 9.314 distance: 66 - 67: 17.465 distance: 67 - 68: 17.964 distance: 67 - 69: 14.148 distance: 70 - 71: 19.645 distance: 71 - 72: 11.470 distance: 71 - 74: 13.200 distance: 72 - 73: 23.964 distance: 72 - 77: 19.939 distance: 74 - 75: 8.154 distance: 74 - 76: 20.651 distance: 77 - 78: 9.224 distance: 78 - 79: 10.481 distance: 78 - 81: 14.535 distance: 79 - 80: 17.379 distance: 79 - 85: 24.070 distance: 81 - 82: 17.087 distance: 82 - 83: 10.288 distance: 82 - 84: 19.899 distance: 85 - 86: 6.708 distance: 85 - 91: 32.624 distance: 86 - 87: 20.462 distance: 86 - 89: 9.271 distance: 87 - 88: 12.563 distance: 87 - 92: 5.305 distance: 89 - 90: 10.700 distance: 90 - 91: 37.707 distance: 92 - 93: 22.535 distance: 93 - 94: 12.448 distance: 93 - 96: 15.621 distance: 94 - 95: 19.746 distance: 94 - 99: 6.946 distance: 95 - 127: 24.520 distance: 96 - 97: 17.814 distance: 96 - 98: 14.997 distance: 99 - 100: 12.297 distance: 100 - 101: 5.406 distance: 100 - 103: 16.895 distance: 101 - 102: 9.703 distance: 102 - 135: 4.800 distance: 103 - 104: 5.319 distance: 104 - 105: 20.287 distance: 104 - 106: 23.154 distance: 107 - 108: 10.334 distance: 108 - 109: 3.850 distance: 108 - 111: 4.700 distance: 109 - 110: 7.391 distance: 109 - 118: 10.608 distance: 110 - 141: 10.654 distance: 111 - 112: 7.692 distance: 112 - 113: 6.702 distance: 112 - 114: 9.161 distance: 113 - 115: 8.150 distance: 114 - 116: 4.527 distance: 115 - 117: 8.398 distance: 116 - 117: 8.734 distance: 118 - 119: 5.835 distance: 119 - 120: 8.763 distance: 119 - 122: 14.886 distance: 120 - 121: 5.627 distance: 120 - 127: 6.190 distance: 121 - 147: 3.760 distance: 122 - 123: 14.668 distance: 123 - 124: 10.658 distance: 124 - 125: 20.311 distance: 125 - 126: 6.069 distance: 128 - 129: 4.320 distance: 128 - 131: 8.318 distance: 129 - 130: 21.969 distance: 129 - 135: 11.006 distance: 130 - 154: 13.024 distance: 131 - 132: 12.985 distance: 132 - 133: 10.833 distance: 132 - 134: 8.884