Starting phenix.real_space_refine on Fri Aug 22 18:31:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdd_45468/08_2025/9cdd_45468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdd_45468/08_2025/9cdd_45468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2025/9cdd_45468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2025/9cdd_45468_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2025/9cdd_45468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2025/9cdd_45468.map" } resolution = 3.05 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= 0.014 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 P 12 5.49 5 S 57 5.16 5 C 4761 2.51 5 N 903 2.21 5 O 1134 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6867 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1954 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 335 Unusual residues: {'CLR': 3, 'PEE': 4, 'RET': 1} Classifications: {'undetermined': 8, 'water': 27} Link IDs: {None: 34} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Restraints were copied for chains: B, C Time building chain proxies: 1.53, per 1000 atoms: 0.22 Number of scatterers: 6867 At special positions: 0 Unit cell: (76.22, 79.31, 76.22, 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) S 57 16.00 P 12 15.00 O 1134 8.00 N 903 7.00 C 4761 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 317.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.515A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.538A pdb=" N CYS A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.605A pdb=" N ARG A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.270A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.745A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.002A pdb=" N TYR A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.514A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.538A pdb=" N CYS B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 167 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.605A pdb=" N ARG B 176 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.270A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.745A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 4.002A pdb=" N TYR B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.515A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 121 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.538A pdb=" N CYS C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 167 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.605A pdb=" N ARG C 176 " --> pdb=" O HIS C 172 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.270A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.745A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 removed outlier: 4.002A pdb=" N TYR C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 372 hydrogen bonds defined for protein. 1116 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: 0.91 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1145 1.33 - 1.45: 1858 1.45 - 1.57: 3873 1.57 - 1.69: 60 1.69 - 1.81: 90 Bond restraints: 7026 Sorted by residual: bond pdb=" O4P PEE A 305 " pdb=" P PEE A 305 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O4P PEE C 305 " pdb=" P PEE C 305 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O4P PEE B 305 " pdb=" P PEE B 305 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O4P PEE B 306 " pdb=" P PEE B 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O4P PEE A 306 " pdb=" P PEE A 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 7021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 9078 2.79 - 5.58: 288 5.58 - 8.37: 81 8.37 - 11.16: 6 11.16 - 13.95: 12 Bond angle restraints: 9465 Sorted by residual: angle pdb=" O1P PEE A 305 " pdb=" P PEE A 305 " pdb=" O2P PEE A 305 " ideal model delta sigma weight residual 119.43 133.38 -13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE C 305 " pdb=" P PEE C 305 " pdb=" O2P PEE C 305 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE B 305 " pdb=" P PEE B 305 " pdb=" O2P PEE B 305 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE A 306 " pdb=" P PEE A 306 " pdb=" O2P PEE A 306 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE C 306 " pdb=" P PEE C 306 " pdb=" O2P PEE C 306 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 ... (remaining 9460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 4236 34.47 - 68.95: 234 68.95 - 103.42: 27 103.42 - 137.90: 15 137.90 - 172.37: 33 Dihedral angle restraints: 4545 sinusoidal: 2451 harmonic: 2094 Sorted by residual: dihedral pdb=" N PEE C 305 " pdb=" C4 PEE C 305 " pdb=" C5 PEE C 305 " pdb=" O4P PEE C 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.40 -172.37 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE B 305 " pdb=" C4 PEE B 305 " pdb=" C5 PEE B 305 " pdb=" O4P PEE B 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.39 -172.36 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE A 305 " pdb=" C4 PEE A 305 " pdb=" C5 PEE A 305 " pdb=" O4P PEE A 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.39 -172.36 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 859 0.086 - 0.172: 47 0.172 - 0.258: 15 0.258 - 0.344: 18 0.344 - 0.430: 18 Chirality restraints: 957 Sorted by residual: chirality pdb=" C2 PEE A 305 " pdb=" C1 PEE A 305 " pdb=" C3 PEE A 305 " pdb=" O2 PEE A 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" C2 PEE C 305 " pdb=" C1 PEE C 305 " pdb=" C3 PEE C 305 " pdb=" O2 PEE C 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2 PEE B 305 " pdb=" C1 PEE B 305 " pdb=" C3 PEE B 305 " pdb=" O2 PEE B 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 954 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 RET B 301 " 0.045 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C7 RET B 301 " -0.043 2.00e-02 2.50e+03 pdb=" C8 RET B 301 " -0.049 2.00e-02 2.50e+03 pdb=" C9 RET B 301 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 RET A 301 " -0.045 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C7 RET A 301 " 0.043 2.00e-02 2.50e+03 pdb=" C8 RET A 301 " 0.049 2.00e-02 2.50e+03 pdb=" C9 RET A 301 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 RET C 301 " 0.045 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C7 RET C 301 " -0.042 2.00e-02 2.50e+03 pdb=" C8 RET C 301 " -0.049 2.00e-02 2.50e+03 pdb=" C9 RET C 301 " 0.046 2.00e-02 2.50e+03 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 0.63 - 1.48: 21 1.48 - 2.34: 51 2.34 - 3.19: 6391 3.19 - 4.05: 18560 4.05 - 4.90: 36464 Warning: very small nonbonded interaction distances. Nonbonded interactions: 61487 Sorted by model distance: nonbonded pdb=" CZ ARG B 62 " pdb=" CG PRO C 124 " model vdw 0.629 3.670 nonbonded pdb=" CZ ARG A 62 " pdb=" CG PRO B 124 " model vdw 0.631 3.670 nonbonded pdb=" CG PRO A 124 " pdb=" CZ ARG C 62 " model vdw 0.637 3.670 nonbonded pdb=" CA PRO A 124 " pdb=" NH1 ARG C 62 " model vdw 0.731 3.550 nonbonded pdb=" NH1 ARG A 62 " pdb=" CA PRO B 124 " model vdw 0.735 3.550 ... (remaining 61482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.120 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.570 Find NCS groups from input model: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 0.478 7032 Z= 1.102 Angle : 1.210 13.948 9465 Z= 0.463 Chirality : 0.085 0.430 957 Planarity : 0.005 0.046 1044 Dihedral : 25.461 172.369 3213 Min Nonbonded Distance : 0.629 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 9.27 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.31), residues: 714 helix: 0.03 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -2.27 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 151 TYR 0.012 0.002 TYR B 103 PHE 0.019 0.002 PHE B 195 TRP 0.009 0.002 TRP B 190 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00933 ( 7026) covalent geometry : angle 1.20987 ( 9465) hydrogen bonds : bond 0.25592 ( 372) hydrogen bonds : angle 7.46603 ( 1116) Misc. bond : bond 0.34311 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.3217 (mtt) cc_final: 0.2998 (mtm) REVERT: A 172 HIS cc_start: 0.7177 (m170) cc_final: 0.6875 (m-70) REVERT: A 187 TRP cc_start: 0.7171 (m100) cc_final: 0.6953 (m100) REVERT: B 51 MET cc_start: 0.4492 (mtt) cc_final: 0.3729 (ttp) REVERT: B 235 ILE cc_start: 0.7388 (mt) cc_final: 0.7089 (mt) REVERT: C 35 PHE cc_start: 0.7394 (t80) cc_final: 0.6479 (t80) REVERT: C 134 PHE cc_start: 0.7570 (t80) cc_final: 0.7313 (t80) REVERT: C 186 ARG cc_start: 0.5362 (ttp-110) cc_final: 0.4960 (ttp80) REVERT: C 234 SER cc_start: 0.8013 (p) cc_final: 0.7488 (m) outliers start: 12 outliers final: 6 residues processed: 184 average time/residue: 0.0711 time to fit residues: 17.6728 Evaluate side-chains 143 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7561 > 50: distance: 12 - 41: 15.845 distance: 23 - 52: 23.954 distance: 27 - 60: 29.543 distance: 31 - 41: 16.841 distance: 41 - 42: 12.290 distance: 42 - 43: 23.018 distance: 42 - 45: 21.036 distance: 43 - 44: 17.244 distance: 43 - 52: 37.458 distance: 45 - 46: 19.280 distance: 46 - 47: 10.472 distance: 47 - 48: 17.720 distance: 48 - 49: 19.198 distance: 49 - 50: 10.203 distance: 49 - 51: 17.460 distance: 52 - 53: 28.429 distance: 53 - 54: 12.153 distance: 53 - 56: 16.780 distance: 54 - 55: 6.495 distance: 54 - 60: 9.152 distance: 56 - 57: 52.175 distance: 57 - 58: 21.869 distance: 57 - 59: 41.024 distance: 60 - 61: 18.637 distance: 61 - 62: 24.854 distance: 61 - 64: 24.741 distance: 62 - 63: 29.067 distance: 62 - 68: 28.956 distance: 64 - 65: 15.580 distance: 65 - 66: 24.991 distance: 65 - 67: 25.652 distance: 68 - 69: 21.080 distance: 69 - 70: 18.009 distance: 69 - 72: 16.324 distance: 70 - 71: 22.275 distance: 70 - 76: 3.947 distance: 72 - 73: 19.450 distance: 73 - 74: 17.442 distance: 73 - 75: 31.262 distance: 76 - 77: 24.675 distance: 77 - 78: 57.286 distance: 78 - 79: 39.851 distance: 78 - 80: 35.816 distance: 80 - 81: 41.243 distance: 81 - 82: 26.666 distance: 81 - 84: 43.340 distance: 82 - 83: 26.361 distance: 82 - 88: 11.598 distance: 84 - 85: 22.447 distance: 85 - 86: 24.494 distance: 86 - 87: 40.289 distance: 88 - 89: 29.260 distance: 89 - 90: 47.963 distance: 90 - 91: 18.633 distance: 90 - 92: 47.087 distance: 92 - 93: 28.587 distance: 93 - 94: 15.690 distance: 93 - 96: 19.273 distance: 94 - 95: 43.983 distance: 94 - 104: 30.243 distance: 96 - 97: 24.651 distance: 97 - 98: 27.531 distance: 97 - 99: 28.858 distance: 98 - 100: 15.880 distance: 99 - 101: 20.086 distance: 100 - 102: 12.851 distance: 101 - 102: 32.242 distance: 102 - 103: 19.424 distance: 104 - 105: 7.352 distance: 105 - 106: 25.313 distance: 105 - 108: 32.133 distance: 106 - 107: 11.235 distance: 106 - 110: 20.861 distance: 108 - 109: 44.978 distance: 110 - 111: 35.276 distance: 111 - 112: 25.467 distance: 111 - 114: 15.035 distance: 112 - 113: 34.094 distance: 112 - 116: 26.809 distance: 114 - 115: 37.008 distance: 156 - 170: 3.004 distance: 165 - 185: 3.140