Starting phenix.real_space_refine on Wed Jul 1 23:33:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2026/7rbu_24402.map" } resolution = 3.7 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= 0.008 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 2629 2.51 5 N 665 2.21 5 O 800 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: 4107 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2241 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" 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: "C" 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.75, per 1000 atoms: 0.18 Number of scatterers: 4107 At special positions: 0 Unit cell: (86.8, 66.64, 81.2, 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 800 8.00 N 665 7.00 C 2629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN B 122 " " NAG B 401 " - " ASN B 234 " " NAG B 402 " - " ASN B 61 " " NAG B 403 " - " ASN B 149 " " NAG C 1 " - " ASN B 17 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 100.6 milliseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.501A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.501A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 76 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.575A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.555A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.266A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.829A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.621A pdb=" N LEU B 176 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 110 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG H 101 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 99 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP H 115 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N CYS H 97 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 37 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER H 52 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.621A pdb=" N LEU B 176 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 110 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG H 101 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 99 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP H 115 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N CYS H 97 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 93 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 121 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.784A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.013A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.330A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 303 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: 0.51 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: 1264 1.34 - 1.47: 1167 1.47 - 1.59: 1771 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 4218 Sorted by residual: bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.30e-02 5.92e+03 8.81e+00 bond pdb=" N PHE B 168 " pdb=" CA PHE B 168 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.10e+00 bond pdb=" N SER B 162 " pdb=" CA SER B 162 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.20e-02 6.94e+03 6.98e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.16e-02 7.43e+03 4.84e+00 ... (remaining 4213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 5204 1.24 - 2.48: 403 2.48 - 3.71: 102 3.71 - 4.95: 25 4.95 - 6.19: 7 Bond angle restraints: 5741 Sorted by residual: angle pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" O ASN B 165 " ideal model delta sigma weight residual 121.84 116.48 5.36 1.16e+00 7.43e-01 2.14e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 113.71 109.41 4.30 9.50e-01 1.11e+00 2.05e+01 angle pdb=" C SER L 56 " pdb=" CA SER L 56 " pdb=" CB SER L 56 " ideal model delta sigma weight residual 116.34 110.15 6.19 1.40e+00 5.10e-01 1.95e+01 angle pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" N CYS B 166 " ideal model delta sigma weight residual 115.51 119.95 -4.44 1.30e+00 5.92e-01 1.17e+01 angle pdb=" CA ASN B 164 " pdb=" C ASN B 164 " pdb=" O ASN B 164 " ideal model delta sigma weight residual 121.38 117.77 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 5736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2186 17.16 - 34.32: 170 34.32 - 51.48: 41 51.48 - 68.64: 4 68.64 - 85.80: 2 Dihedral angle restraints: 2403 sinusoidal: 925 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 151.53 -58.53 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA CYS B 136 " pdb=" C CYS B 136 " pdb=" N ASN B 137 " pdb=" CA ASN B 137 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 2400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 462 0.046 - 0.092: 136 0.092 - 0.138: 42 0.138 - 0.184: 5 0.184 - 0.230: 2 Chirality restraints: 647 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU B 169 " pdb=" N GLU B 169 " pdb=" C GLU B 169 " pdb=" CB GLU B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA SER L 7 " pdb=" N SER L 7 " pdb=" C SER L 7 " pdb=" CB SER L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 644 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.81e+00 pdb=" N PRO B 209 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO L 59 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 161 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C SER B 161 " -0.026 2.00e-02 2.50e+03 pdb=" O SER B 161 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 162 " 0.009 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 204 2.71 - 3.26: 3673 3.26 - 3.81: 5933 3.81 - 4.35: 6871 4.35 - 4.90: 12578 Nonbonded interactions: 29259 Sorted by model distance: nonbonded pdb=" OG SER L 52 " pdb=" O GLY L 64 " model vdw 2.167 3.040 nonbonded pdb=" O ASN B 17 " pdb=" OG SER B 255 " model vdw 2.211 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 79 " model vdw 2.229 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" OE2 GLU L 81 " model vdw 2.231 3.120 nonbonded pdb=" OG SER L 12 " pdb=" OE2 GLU L 105 " model vdw 2.275 3.040 ... (remaining 29254 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' } 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: 0.010 Normalize map: mean=0, sd=1: 24.700 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.730 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 0.043 4229 Z= 0.269 Angle : 0.826 7.155 5770 Z= 0.462 Chirality : 0.049 0.230 647 Planarity : 0.005 0.055 721 Dihedral : 12.526 68.971 1451 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.13 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -2.50 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.06 (0.38), residues: 196 loop : -3.05 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.021 0.002 TYR B 204 PHE 0.021 0.002 PHE B 59 TRP 0.017 0.002 TRP H 117 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.27 ( 4218) covalent geometry : angle 0.80236 / 0.46 ( 5741) SS BOND : bond 0.01351 / 0.65 ( 4) SS BOND : angle 3.12040 / 1.81 ( 8) hydrogen bonds : bond 0.19615 / 13.11 ( 109) hydrogen bonds : angle 7.26158 / 4.58 ( 303) link_BETA1-4 : bond 0.00037 / 0.02 ( 2) link_BETA1-4 : angle 2.55091 / 1.42 ( 6) link_NAG-ASN : bond 0.00342 / 0.18 ( 5) link_NAG-ASN : angle 2.87375 / 1.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.104 Fit side-chains REVERT: H 110 SER cc_start: 0.7742 (p) cc_final: 0.7538 (p) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0407 time to fit residues: 3.5890 Evaluate side-chains 58 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099899 restraints weight = 6359.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103348 restraints weight = 3404.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105597 restraints weight = 2265.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106850 restraints weight = 1737.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107885 restraints weight = 1476.846| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4229 Z= 0.144 Angle : 0.683 9.460 5770 Z= 0.344 Chirality : 0.044 0.213 647 Planarity : 0.004 0.046 721 Dihedral : 4.945 18.531 556 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.73 % Favored : 91.07 % Rotamer: Outliers : 1.79 % Allowed : 7.85 % Favored : 90.36 % 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: -2.22 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.23 (0.37), residues: 207 loop : -2.96 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.016 0.002 TYR B 204 PHE 0.012 0.002 PHE H 80 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4218) covalent geometry : angle 0.66782 / 0.34 ( 5741) SS BOND : bond 0.00571 / 0.28 ( 4) SS BOND : angle 1.87581 / 1.05 ( 8) hydrogen bonds : bond 0.05793 / 3.89 ( 109) hydrogen bonds : angle 6.13402 / 3.96 ( 303) link_BETA1-4 : bond 0.00557 / 0.28 ( 2) link_BETA1-4 : angle 2.23896 / 1.28 ( 6) link_NAG-ASN : bond 0.00143 / 0.07 ( 5) link_NAG-ASN : angle 2.21904 / 1.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.103 Fit side-chains REVERT: B 97 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8037 (mtmm) REVERT: B 278 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7188 (ttpp) outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.0500 time to fit residues: 4.8216 Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 24 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.0670 chunk 31 optimal weight: 0.0170 overall best weight: 0.0446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103434 restraints weight = 6337.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106762 restraints weight = 3504.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108820 restraints weight = 2377.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110375 restraints weight = 1855.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111194 restraints weight = 1561.631| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4229 Z= 0.100 Angle : 0.619 9.470 5770 Z= 0.304 Chirality : 0.043 0.228 647 Planarity : 0.004 0.042 721 Dihedral : 4.600 20.678 556 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.57 % Allowed : 13.45 % Favored : 84.98 % 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: -2.07 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.34 (0.37), residues: 209 loop : -2.88 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 99 TYR 0.016 0.001 TYR B 265 PHE 0.014 0.001 PHE B 133 TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 4218) covalent geometry : angle 0.59982 / 0.30 ( 5741) SS BOND : bond 0.00433 / 0.21 ( 4) SS BOND : angle 2.35948 / 1.36 ( 8) hydrogen bonds : bond 0.03910 / 2.60 ( 109) hydrogen bonds : angle 5.76691 / 3.75 ( 303) link_BETA1-4 : bond 0.00383 / 0.20 ( 2) link_BETA1-4 : angle 2.28757 / 1.31 ( 6) link_NAG-ASN : bond 0.00115 / 0.06 ( 5) link_NAG-ASN : angle 2.14474 / 1.18 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7985 (mtmm) REVERT: B 278 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7156 (ttpp) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.0414 time to fit residues: 3.1951 Evaluate side-chains 59 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 24 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098527 restraints weight = 6334.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101861 restraints weight = 3463.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103906 restraints weight = 2339.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105439 restraints weight = 1827.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106474 restraints weight = 1527.825| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4229 Z= 0.239 Angle : 0.736 9.534 5770 Z= 0.373 Chirality : 0.045 0.250 647 Planarity : 0.005 0.050 721 Dihedral : 5.200 21.782 556 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.91 % Allowed : 15.92 % Favored : 81.17 % 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: -2.14 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.36 (0.37), residues: 205 loop : -2.95 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.024 0.002 TYR B 204 PHE 0.022 0.003 PHE B 59 TRP 0.008 0.002 TRP L 32 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 ( 4218) covalent geometry : angle 0.71430 / 0.37 ( 5741) SS BOND : bond 0.00809 / 0.40 ( 4) SS BOND : angle 3.42249 / 1.99 ( 8) hydrogen bonds : bond 0.07084 / 4.72 ( 109) hydrogen bonds : angle 5.96924 / 3.89 ( 303) link_BETA1-4 : bond 0.00462 / 0.23 ( 2) link_BETA1-4 : angle 1.87481 / 1.08 ( 6) link_NAG-ASN : bond 0.00221 / 0.12 ( 5) link_NAG-ASN : angle 2.28008 / 1.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8064 (mtmm) REVERT: B 278 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7193 (ttpp) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.0452 time to fit residues: 4.1884 Evaluate side-chains 75 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 78 LEU 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: 70.1038 > 50: distance: 65 - 71: 16.575 distance: 71 - 72: 20.162 distance: 72 - 73: 25.050 distance: 72 - 75: 10.722 distance: 73 - 74: 16.463 distance: 73 - 78: 24.303 distance: 75 - 76: 20.812 distance: 75 - 77: 16.121 distance: 78 - 79: 43.783 distance: 79 - 80: 19.309 distance: 79 - 82: 44.467 distance: 80 - 81: 21.122 distance: 80 - 89: 21.385 distance: 82 - 83: 29.160 distance: 83 - 84: 59.582 distance: 84 - 85: 42.354 distance: 85 - 86: 14.889 distance: 86 - 87: 3.046 distance: 86 - 88: 12.800 distance: 89 - 90: 21.297 distance: 90 - 91: 20.120 distance: 90 - 93: 60.418 distance: 91 - 97: 69.337 distance: 94 - 95: 56.407 distance: 94 - 96: 56.245 distance: 97 - 98: 38.324 distance: 98 - 99: 31.510 distance: 98 - 101: 23.295 distance: 99 - 100: 20.759 distance: 99 - 105: 16.698 distance: 101 - 102: 39.416 distance: 102 - 103: 14.290 distance: 102 - 104: 14.362 distance: 105 - 106: 10.402 distance: 105 - 111: 30.831 distance: 106 - 107: 25.362 distance: 106 - 109: 34.483 distance: 107 - 108: 23.363 distance: 107 - 112: 40.716 distance: 109 - 110: 19.961 distance: 110 - 111: 23.664 distance: 112 - 113: 14.435 distance: 113 - 114: 36.380 distance: 113 - 116: 59.720 distance: 114 - 115: 40.490 distance: 114 - 121: 16.684 distance: 116 - 117: 11.475 distance: 117 - 118: 40.985 distance: 118 - 119: 42.151 distance: 118 - 120: 41.349 distance: 121 - 122: 48.522 distance: 122 - 123: 23.974 distance: 123 - 124: 49.783 distance: 123 - 125: 43.798 distance: 125 - 126: 21.147 distance: 126 - 127: 12.601 distance: 126 - 129: 22.540 distance: 127 - 128: 41.597 distance: 127 - 136: 10.454 distance: 129 - 130: 40.563 distance: 130 - 131: 3.400 distance: 130 - 132: 11.906 distance: 131 - 133: 13.342 distance: 132 - 134: 42.693 distance: 133 - 135: 39.282 distance: 134 - 135: 52.302 distance: 136 - 137: 20.298 distance: 137 - 138: 42.735 distance: 137 - 140: 47.669 distance: 138 - 139: 53.051 distance: 138 - 142: 25.737 distance: 140 - 141: 8.445 distance: 142 - 143: 25.672 distance: 143 - 144: 14.359 distance: 143 - 146: 42.692 distance: 144 - 145: 45.099 distance: 144 - 147: 20.094