Starting phenix.real_space_refine on Wed Jul 1 23:28:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm4_27526/07_2026/8dm4_27526.cif" } resolution = 2.45 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= -0.001 sd= 0.017 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 18 5.16 5 C 2563 2.51 5 N 653 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4018 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.76, per 1000 atoms: 0.19 Number of scatterers: 4018 At special positions: 0 Unit cell: (101, 61, 97, 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 18 16.00 O 784 8.00 N 653 7.00 C 2563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 142.4 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 10 sheets defined 1.6% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.905A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.766A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.711A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 102 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 4.284A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 0.56 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1249 1.34 - 1.46: 1064 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 4117 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 4112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5350 2.08 - 4.16: 220 4.16 - 6.23: 18 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 5594 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" C LEU A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 122.93 118.21 4.72 1.45e+00 4.76e-01 1.06e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.47 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.29e+00 angle pdb=" N THR L 34 " pdb=" CA THR L 34 " pdb=" C THR L 34 " ideal model delta sigma weight residual 110.35 106.53 3.82 1.38e+00 5.25e-01 7.64e+00 ... (remaining 5589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2191 17.82 - 35.63: 141 35.63 - 53.45: 26 53.45 - 71.27: 6 71.27 - 89.09: 4 Dihedral angle restraints: 2368 sinusoidal: 925 harmonic: 1443 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -51.05 -34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA VAL H 24 " pdb=" C VAL H 24 " pdb=" N GLU H 25 " pdb=" CA GLU H 25 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 424 0.051 - 0.102: 159 0.102 - 0.152: 44 0.152 - 0.203: 4 0.203 - 0.254: 3 Chirality restraints: 634 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 631 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 27 " -0.048 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO L 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 28 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 28 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.237 9.50e-02 1.11e+02 1.07e-01 7.74e+00 pdb=" NE ARG A 273 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C ILE A 210 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 865 2.79 - 3.32: 3144 3.32 - 3.84: 6623 3.84 - 4.37: 7758 4.37 - 4.90: 13925 Nonbonded interactions: 32315 Sorted by model distance: nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.279 3.040 nonbonded pdb=" O SER L 45 " pdb=" OG1 THR L 94 " model vdw 2.307 3.040 nonbonded pdb=" OG SER A 247 " pdb=" OH TYR H 46 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.368 3.040 ... (remaining 32310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.960 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.045 4127 Z= 0.271 Angle : 0.925 10.390 5620 Z= 0.489 Chirality : 0.057 0.254 634 Planarity : 0.008 0.107 706 Dihedral : 13.134 89.087 1432 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.05 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.55 (0.34), residues: 230 loop : -0.55 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 273 TYR 0.032 0.003 TYR A 145 PHE 0.025 0.003 PHE A 175 TRP 0.021 0.003 TRP H 66 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 ( 4117) covalent geometry : angle 0.90354 / 0.48 ( 5594) SS BOND : bond 0.00341 / 0.16 ( 4) SS BOND : angle 2.19227 / 1.16 ( 8) hydrogen bonds : bond 0.07968 / 5.01 ( 153) hydrogen bonds : angle 6.59570 / 4.75 ( 399) link_BETA1-4 : bond 0.01012 / 0.53 ( 1) link_BETA1-4 : angle 2.50579 / 1.31 ( 3) link_NAG-ASN : bond 0.00372 / 0.21 ( 5) link_NAG-ASN : angle 3.54620 / 2.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.164 Fit side-chains REVERT: A 80 ASP cc_start: 0.6299 (t0) cc_final: 0.6086 (t0) REVERT: A 100 ILE cc_start: 0.8408 (mp) cc_final: 0.8064 (tp) REVERT: H 52 SER cc_start: 0.7982 (m) cc_final: 0.7705 (p) REVERT: H 65 GLU cc_start: 0.6701 (pt0) cc_final: 0.6168 (pm20) REVERT: H 107 SER cc_start: 0.7089 (m) cc_final: 0.6425 (t) REVERT: H 131 TYR cc_start: 0.8106 (t80) cc_final: 0.7868 (t80) REVERT: H 134 MET cc_start: 0.8612 (mtm) cc_final: 0.8405 (mpp) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.4090 time to fit residues: 42.3594 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 30 ASN L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.145299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101556 restraints weight = 5703.054| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.20 r_work: 0.3227 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4127 Z= 0.132 Angle : 0.599 8.293 5620 Z= 0.306 Chirality : 0.044 0.198 634 Planarity : 0.004 0.055 706 Dihedral : 4.813 16.954 539 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.75 % Allowed : 10.76 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.31 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.78 (0.35), residues: 215 loop : -0.23 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.013 0.002 TYR A 28 PHE 0.014 0.001 PHE A 175 TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4117) covalent geometry : angle 0.57994 / 0.30 ( 5594) SS BOND : bond 0.00212 / 0.11 ( 4) SS BOND : angle 1.46937 / 0.75 ( 8) hydrogen bonds : bond 0.03652 / 2.37 ( 153) hydrogen bonds : angle 5.95904 / 4.22 ( 399) link_BETA1-4 : bond 0.00192 / 0.10 ( 1) link_BETA1-4 : angle 1.22723 / 0.63 ( 3) link_NAG-ASN : bond 0.00191 / 0.10 ( 5) link_NAG-ASN : angle 2.70669 / 1.69 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.146 Fit side-chains REVERT: A 80 ASP cc_start: 0.6572 (t0) cc_final: 0.6106 (t0) REVERT: A 169 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: A 173 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: H 65 GLU cc_start: 0.7362 (pt0) cc_final: 0.6724 (pm20) REVERT: H 100 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6551 (ttp) REVERT: H 109 ASP cc_start: 0.7134 (t0) cc_final: 0.6867 (t0) REVERT: H 131 TYR cc_start: 0.8151 (t80) cc_final: 0.7898 (t80) REVERT: H 134 MET cc_start: 0.8755 (mtm) cc_final: 0.8458 (mpp) REVERT: L 132 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7371 (mmmm) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.5488 time to fit residues: 41.3608 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 66 HIS L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098963 restraints weight = 5639.211| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.20 r_work: 0.3187 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4127 Z= 0.188 Angle : 0.619 5.744 5620 Z= 0.319 Chirality : 0.045 0.198 634 Planarity : 0.004 0.047 706 Dihedral : 4.814 17.785 539 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 12.81 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.37 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.78 (0.35), residues: 215 loop : -0.15 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.014 0.002 TYR A 28 PHE 0.023 0.002 PHE A 175 TRP 0.013 0.002 TRP H 66 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 4117) covalent geometry : angle 0.59906 / 0.31 ( 5594) SS BOND : bond 0.00310 / 0.15 ( 4) SS BOND : angle 1.53715 / 0.78 ( 8) hydrogen bonds : bond 0.03840 / 2.49 ( 153) hydrogen bonds : angle 5.94441 / 4.19 ( 399) link_BETA1-4 : bond 0.00454 / 0.24 ( 1) link_BETA1-4 : angle 1.15609 / 0.62 ( 3) link_NAG-ASN : bond 0.00235 / 0.13 ( 5) link_NAG-ASN : angle 2.87011 / 1.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.096 Fit side-chains REVERT: A 14 GLN cc_start: 0.7702 (mt0) cc_final: 0.7454 (mt0) REVERT: A 80 ASP cc_start: 0.6676 (t0) cc_final: 0.6217 (t0) REVERT: A 115 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8220 (mm110) REVERT: A 137 ASN cc_start: 0.8466 (m110) cc_final: 0.7982 (t0) REVERT: A 169 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: A 173 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: A 177 MET cc_start: 0.7947 (pmt) cc_final: 0.7652 (pmt) REVERT: H 65 GLU cc_start: 0.7466 (pt0) cc_final: 0.7125 (pt0) REVERT: H 78 MET cc_start: 0.7049 (tpp) cc_final: 0.6092 (tpt) REVERT: H 100 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7040 (ttp) REVERT: H 109 ASP cc_start: 0.7365 (t0) cc_final: 0.7113 (t0) REVERT: H 131 TYR cc_start: 0.8226 (t80) cc_final: 0.7922 (t80) REVERT: H 134 MET cc_start: 0.8778 (mtm) cc_final: 0.8478 (mpp) REVERT: L 98 LEU cc_start: 0.6911 (tp) cc_final: 0.6688 (tp) REVERT: L 117 THR cc_start: 0.8388 (p) cc_final: 0.8148 (p) REVERT: L 132 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7388 (mmmm) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.5317 time to fit residues: 40.0731 Evaluate side-chains 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.143093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099291 restraints weight = 5582.999| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.22 r_work: 0.3198 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4127 Z= 0.166 Angle : 0.594 6.388 5620 Z= 0.306 Chirality : 0.045 0.192 634 Planarity : 0.004 0.043 706 Dihedral : 4.698 17.289 539 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.52 % Allowed : 13.96 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.50 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.87 (0.35), residues: 212 loop : -0.04 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.013 0.002 TYR A 28 PHE 0.020 0.002 PHE A 175 TRP 0.012 0.001 TRP H 66 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 4117) covalent geometry : angle 0.57385 / 0.30 ( 5594) SS BOND : bond 0.00327 / 0.16 ( 4) SS BOND : angle 1.65173 / 0.83 ( 8) hydrogen bonds : bond 0.03657 / 2.37 ( 153) hydrogen bonds : angle 5.84796 / 4.12 ( 399) link_BETA1-4 : bond 0.00222 / 0.12 ( 1) link_BETA1-4 : angle 0.99287 / 0.54 ( 3) link_NAG-ASN : bond 0.00231 / 0.13 ( 5) link_NAG-ASN : angle 2.77787 / 1.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.153 Fit side-chains REVERT: A 80 ASP cc_start: 0.6698 (t0) cc_final: 0.6239 (t0) REVERT: A 137 ASN cc_start: 0.8501 (m110) cc_final: 0.8035 (t0) REVERT: A 169 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: A 173 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: H 65 GLU cc_start: 0.7488 (pt0) cc_final: 0.7146 (pt0) REVERT: H 78 MET cc_start: 0.7041 (tpp) cc_final: 0.6107 (tpt) REVERT: H 100 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7085 (ttp) REVERT: H 134 MET cc_start: 0.8742 (mtm) cc_final: 0.8477 (mpp) REVERT: L 60 TRP cc_start: 0.8448 (m100) cc_final: 0.8247 (m100) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.5080 time to fit residues: 38.3762 Evaluate side-chains 70 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8794 > 50: distance: 68 - 179: 11.076 distance: 71 - 176: 4.274 distance: 92 - 115: 13.446 distance: 95 - 112: 16.738 distance: 104 - 112: 16.979 distance: 112 - 113: 7.443 distance: 113 - 114: 4.532 distance: 113 - 116: 9.791 distance: 114 - 115: 11.377 distance: 114 - 120: 6.808 distance: 116 - 117: 8.386 distance: 117 - 118: 17.031 distance: 117 - 119: 15.637 distance: 120 - 121: 6.662 distance: 121 - 122: 10.299 distance: 121 - 124: 6.403 distance: 122 - 123: 4.816 distance: 122 - 132: 11.813 distance: 124 - 125: 14.961 distance: 125 - 126: 13.176 distance: 125 - 127: 14.143 distance: 126 - 128: 14.812 distance: 127 - 129: 18.893 distance: 128 - 130: 10.969 distance: 129 - 130: 16.632 distance: 130 - 131: 5.146 distance: 132 - 133: 8.024 distance: 133 - 134: 10.734 distance: 133 - 136: 7.126 distance: 134 - 135: 7.237 distance: 136 - 137: 11.832 distance: 137 - 138: 16.422 distance: 137 - 139: 9.133 distance: 138 - 140: 12.057 distance: 139 - 141: 9.362 distance: 140 - 142: 9.855 distance: 141 - 142: 9.698 distance: 142 - 143: 4.178 distance: 144 - 145: 19.156 distance: 145 - 146: 21.665 distance: 145 - 148: 7.520 distance: 146 - 147: 22.229 distance: 146 - 156: 28.142 distance: 148 - 149: 6.821 distance: 149 - 150: 3.757 distance: 149 - 151: 6.400 distance: 150 - 152: 7.220 distance: 151 - 153: 8.805 distance: 152 - 154: 9.374 distance: 153 - 154: 9.332 distance: 154 - 155: 6.657 distance: 156 - 157: 32.768 distance: 157 - 158: 17.451 distance: 158 - 159: 21.368 distance: 158 - 160: 17.071 distance: 160 - 161: 7.823 distance: 161 - 162: 9.987 distance: 161 - 164: 8.209 distance: 162 - 163: 16.090 distance: 162 - 168: 12.228 distance: 164 - 165: 19.803 distance: 165 - 166: 36.140 distance: 166 - 167: 11.909 distance: 169 - 170: 18.611 distance: 169 - 172: 9.316 distance: 170 - 171: 8.358 distance: 170 - 176: 4.008 distance: 172 - 173: 7.658 distance: 173 - 174: 16.184 distance: 173 - 175: 8.678 distance: 176 - 177: 6.108 distance: 177 - 178: 9.590 distance: 177 - 180: 5.071 distance: 178 - 179: 10.219 distance: 178 - 183: 6.115 distance: 180 - 181: 13.647 distance: 180 - 182: 14.662 distance: 183 - 184: 5.715 distance: 184 - 185: 10.590 distance: 184 - 187: 6.782 distance: 185 - 186: 16.103 distance: 185 - 197: 18.705 distance: 187 - 188: 3.335 distance: 188 - 189: 5.091 distance: 188 - 190: 8.769 distance: 189 - 191: 3.278 distance: 190 - 192: 3.926 distance: 190 - 193: 8.707 distance: 191 - 192: 8.796 distance: 192 - 194: 7.052 distance: 193 - 195: 6.546 distance: 194 - 196: 6.465 distance: 197 - 198: 56.879 distance: 198 - 199: 26.357 distance: 199 - 200: 14.994 distance: 199 - 201: 24.054