Starting phenix.real_space_refine on Fri Aug 22 14:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh1_61469/08_2025/9jh1_61469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh1_61469/08_2025/9jh1_61469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh1_61469/08_2025/9jh1_61469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh1_61469/08_2025/9jh1_61469.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh1_61469/08_2025/9jh1_61469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh1_61469/08_2025/9jh1_61469.cif" } resolution = 3.07 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= 0.042 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 K 2 8.98 5 S 32 5.16 5 C 2799 2.51 5 N 705 2.21 5 O 717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s 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: 4255 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2095 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2102 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, 'EIC': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, 'EIC': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.38, per 1000 atoms: 0.32 Number of scatterers: 4255 At special positions: 0 Unit cell: (68.036, 88.54, 95.064, 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) K 2 19.00 S 32 16.00 O 717 8.00 N 705 7.00 C 2799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 147.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 23 through 63 removed outlier: 3.582A pdb=" N GLU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 167 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 298 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 63 removed outlier: 3.582A pdb=" N GLU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 167 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 298 346 hydrogen bonds defined for protein. 1038 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: 0.57 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1303 1.34 - 1.46: 1024 1.46 - 1.58: 1985 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 4356 Sorted by residual: bond pdb=" C10 EIC A 402 " pdb=" C9 EIC A 402 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" C12 EIC A 402 " pdb=" C13 EIC A 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.53e+01 bond pdb=" C10 EIC B 402 " pdb=" C9 EIC B 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C31 POV A 401 " pdb=" O31 POV A 401 " ideal model delta sigma weight residual 1.327 1.261 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 4351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 5748 3.18 - 6.35: 100 6.35 - 9.53: 11 9.53 - 12.70: 7 12.70 - 15.88: 8 Bond angle restraints: 5874 Sorted by residual: angle pdb=" C12 EIC A 402 " pdb=" C13 EIC A 402 " pdb=" C14 EIC A 402 " ideal model delta sigma weight residual 128.16 112.28 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " pdb=" C14 EIC B 402 " ideal model delta sigma weight residual 128.16 112.28 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C10 EIC A 402 " pdb=" C9 EIC A 402 " pdb=" C8 EIC A 402 " ideal model delta sigma weight residual 127.75 112.16 15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C10 EIC B 402 " pdb=" C9 EIC B 402 " pdb=" C8 EIC B 402 " ideal model delta sigma weight residual 127.75 112.23 15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C11 EIC B 402 " pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " ideal model delta sigma weight residual 127.66 112.40 15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 5869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 2134 19.80 - 39.60: 306 39.60 - 59.40: 54 59.40 - 79.20: 10 79.20 - 98.99: 8 Dihedral angle restraints: 2512 sinusoidal: 995 harmonic: 1517 Sorted by residual: dihedral pdb=" CA ARG B 87 " pdb=" C ARG B 87 " pdb=" N VAL B 88 " pdb=" CA VAL B 88 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ARG A 87 " pdb=" C ARG A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ARG B 92 " pdb=" C ARG B 92 " pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 2509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 487 0.043 - 0.087: 122 0.087 - 0.130: 26 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 645 Sorted by residual: chirality pdb=" CA GLU B 42 " pdb=" N GLU B 42 " pdb=" C GLU B 42 " pdb=" CB GLU B 42 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU A 42 " pdb=" N GLU A 42 " pdb=" C GLU A 42 " pdb=" CB GLU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE B 283 " pdb=" CA ILE B 283 " pdb=" CG1 ILE B 283 " pdb=" CG2 ILE B 283 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 642 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIC A 402 " -0.355 2.00e-02 2.50e+03 3.43e-01 1.18e+03 pdb=" C12 EIC A 402 " 0.383 2.00e-02 2.50e+03 pdb=" C13 EIC A 402 " 0.300 2.00e-02 2.50e+03 pdb=" C14 EIC A 402 " -0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 EIC B 402 " 0.352 2.00e-02 2.50e+03 3.43e-01 1.17e+03 pdb=" C12 EIC B 402 " -0.373 2.00e-02 2.50e+03 pdb=" C13 EIC B 402 " -0.311 2.00e-02 2.50e+03 pdb=" C14 EIC B 402 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIC A 402 " 0.439 2.00e-02 2.50e+03 3.29e-01 1.08e+03 pdb=" C11 EIC A 402 " -0.158 2.00e-02 2.50e+03 pdb=" C8 EIC A 402 " 0.156 2.00e-02 2.50e+03 pdb=" C9 EIC A 402 " -0.437 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 189 2.71 - 3.32: 5444 3.32 - 3.93: 8454 3.93 - 4.53: 10968 4.53 - 5.14: 16369 Nonbonded interactions: 41424 Sorted by model distance: nonbonded pdb=" OE2 GLU A 220 " pdb=" OH TYR A 257 " model vdw 2.104 3.040 nonbonded pdb=" OE2 GLU B 220 " pdb=" OH TYR B 257 " model vdw 2.104 3.040 nonbonded pdb=" CG2 THR A 237 " pdb=" K K A 403 " model vdw 2.220 3.270 nonbonded pdb=" CG2 THR B 237 " pdb=" K K A 403 " model vdw 2.236 3.270 nonbonded pdb=" OD1 ASP A 89 " pdb=" NH2 ARG B 72 " model vdw 2.250 3.120 ... (remaining 41419 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 'B' and (resid 18 through 299 or resid 401 through 403)) } 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: 1.270 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.008 0.196 4356 Z= 0.383 Angle : 1.141 15.879 5874 Z= 0.526 Chirality : 0.043 0.217 645 Planarity : 0.027 0.343 728 Dihedral : 18.632 98.995 1542 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.81 % Allowed : 34.76 % Favored : 63.43 % 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: -0.19 (0.36), residues: 517 helix: 0.52 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -2.57 (0.58), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG B 56 TYR 0.013 0.002 TYR B 155 PHE 0.008 0.001 PHE B 38 TRP 0.061 0.006 TRP A 95 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00780 ( 4356) covalent geometry : angle 1.14055 ( 5874) hydrogen bonds : bond 0.08409 ( 346) hydrogen bonds : angle 5.33111 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.8281 (mt) cc_final: 0.7699 (mm) REVERT: A 70 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 273 TYR cc_start: 0.8557 (t80) cc_final: 0.8163 (t80) REVERT: B 21 LEU cc_start: 0.8227 (mt) cc_final: 0.7548 (mt) REVERT: B 48 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 70 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 213 SER cc_start: 0.9059 (m) cc_final: 0.8751 (p) REVERT: B 289 TRP cc_start: 0.5463 (t60) cc_final: 0.4904 (t60) outliers start: 8 outliers final: 2 residues processed: 167 average time/residue: 0.0669 time to fit residues: 14.0598 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.0000 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116517 restraints weight = 8232.831| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.57 r_work: 0.3463 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4356 Z= 0.155 Angle : 0.678 9.313 5874 Z= 0.343 Chirality : 0.037 0.171 645 Planarity : 0.004 0.037 728 Dihedral : 8.293 72.272 625 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.61 % Allowed : 29.12 % Favored : 67.27 % 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: 1.45 (0.38), residues: 517 helix: 1.65 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -1.91 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 56 TYR 0.029 0.002 TYR B 30 PHE 0.008 0.001 PHE B 225 TRP 0.018 0.002 TRP A 95 HIS 0.010 0.002 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4356) covalent geometry : angle 0.67818 ( 5874) hydrogen bonds : bond 0.04015 ( 346) hydrogen bonds : angle 4.28243 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7772 (mt) cc_final: 0.7521 (mt) REVERT: A 95 TRP cc_start: 0.4535 (t60) cc_final: 0.4163 (t60) REVERT: A 229 TYR cc_start: 0.8909 (t80) cc_final: 0.8440 (t80) REVERT: A 242 ASP cc_start: 0.8708 (p0) cc_final: 0.8388 (p0) REVERT: B 95 TRP cc_start: 0.4511 (t60) cc_final: 0.4259 (t60) REVERT: B 229 TYR cc_start: 0.8874 (t80) cc_final: 0.8382 (t80) REVERT: B 242 ASP cc_start: 0.8624 (p0) cc_final: 0.8289 (p0) REVERT: B 273 TYR cc_start: 0.8764 (t80) cc_final: 0.8435 (t80) outliers start: 16 outliers final: 8 residues processed: 168 average time/residue: 0.0696 time to fit residues: 14.8056 Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112521 restraints weight = 8305.590| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.62 r_work: 0.3378 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4356 Z= 0.165 Angle : 0.691 9.774 5874 Z= 0.342 Chirality : 0.038 0.156 645 Planarity : 0.004 0.041 728 Dihedral : 5.984 38.230 619 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.61 % Allowed : 29.80 % Favored : 66.59 % 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: 2.04 (0.38), residues: 517 helix: 2.03 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -1.55 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 56 TYR 0.017 0.001 TYR A 30 PHE 0.009 0.001 PHE B 225 TRP 0.009 0.002 TRP A 95 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4356) covalent geometry : angle 0.69092 ( 5874) hydrogen bonds : bond 0.04035 ( 346) hydrogen bonds : angle 4.21238 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8256 (mm-30) REVERT: A 162 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8702 (tp-100) REVERT: A 220 GLU cc_start: 0.8379 (mp0) cc_final: 0.8158 (mp0) REVERT: A 229 TYR cc_start: 0.9012 (t80) cc_final: 0.8411 (t80) REVERT: B 95 TRP cc_start: 0.5059 (t60) cc_final: 0.4843 (t60) REVERT: B 220 GLU cc_start: 0.8407 (mp0) cc_final: 0.8161 (mp0) REVERT: B 273 TYR cc_start: 0.8832 (t80) cc_final: 0.8465 (t80) outliers start: 16 outliers final: 12 residues processed: 165 average time/residue: 0.0506 time to fit residues: 11.3788 Evaluate side-chains 155 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111369 restraints weight = 8292.769| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.55 r_work: 0.3345 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4356 Z= 0.150 Angle : 0.694 14.359 5874 Z= 0.337 Chirality : 0.038 0.155 645 Planarity : 0.004 0.031 728 Dihedral : 5.534 34.177 619 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.84 % Allowed : 30.47 % Favored : 65.69 % 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: 2.39 (0.39), residues: 517 helix: 2.19 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.94 (0.69), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 56 TYR 0.017 0.001 TYR B 30 PHE 0.009 0.001 PHE B 38 TRP 0.023 0.002 TRP A 95 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4356) covalent geometry : angle 0.69447 ( 5874) hydrogen bonds : bond 0.03822 ( 346) hydrogen bonds : angle 4.09009 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8681 (pt0) cc_final: 0.8464 (pp30) REVERT: A 129 PHE cc_start: 0.8493 (m-80) cc_final: 0.8267 (m-80) REVERT: A 158 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8958 (mmtt) REVERT: A 220 GLU cc_start: 0.8342 (mp0) cc_final: 0.8112 (mp0) REVERT: A 229 TYR cc_start: 0.9060 (t80) cc_final: 0.8403 (t80) REVERT: A 242 ASP cc_start: 0.8450 (p0) cc_final: 0.8124 (p0) REVERT: B 70 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 229 TYR cc_start: 0.9047 (t80) cc_final: 0.8437 (t80) REVERT: B 273 TYR cc_start: 0.8846 (t80) cc_final: 0.8432 (t80) outliers start: 17 outliers final: 12 residues processed: 168 average time/residue: 0.0506 time to fit residues: 11.4230 Evaluate side-chains 164 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109046 restraints weight = 8337.297| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.64 r_work: 0.3329 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4356 Z= 0.146 Angle : 0.720 14.713 5874 Z= 0.341 Chirality : 0.038 0.162 645 Planarity : 0.003 0.030 728 Dihedral : 5.324 31.958 619 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.06 % Allowed : 31.38 % Favored : 64.56 % 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: 2.65 (0.39), residues: 517 helix: 2.34 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.69 (0.72), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.027 0.001 TYR B 30 PHE 0.009 0.001 PHE A 103 TRP 0.023 0.002 TRP B 95 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4356) covalent geometry : angle 0.72009 ( 5874) hydrogen bonds : bond 0.03750 ( 346) hydrogen bonds : angle 4.06768 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.8496 (m-80) cc_final: 0.8108 (m-80) REVERT: A 158 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9023 (mmtt) REVERT: A 162 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8541 (tp-100) REVERT: A 215 MET cc_start: 0.9439 (ttp) cc_final: 0.8944 (ttp) REVERT: A 220 GLU cc_start: 0.8345 (mp0) cc_final: 0.8072 (mp0) REVERT: B 70 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 77 HIS cc_start: 0.6242 (t-170) cc_final: 0.5984 (t-170) REVERT: B 129 PHE cc_start: 0.8553 (m-80) cc_final: 0.8181 (m-80) REVERT: B 229 TYR cc_start: 0.9075 (t80) cc_final: 0.8396 (t80) REVERT: B 273 TYR cc_start: 0.8900 (t80) cc_final: 0.8470 (t80) outliers start: 18 outliers final: 13 residues processed: 164 average time/residue: 0.0594 time to fit residues: 12.9159 Evaluate side-chains 158 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.492 > 50: distance: 62 - 76: 30.449 distance: 66 - 83: 31.135 distance: 70 - 94: 35.352 distance: 73 - 76: 32.787 distance: 74 - 100: 34.525 distance: 76 - 77: 33.231 distance: 77 - 78: 41.531 distance: 77 - 80: 43.766 distance: 78 - 79: 24.735 distance: 78 - 83: 11.290 distance: 79 - 105: 29.700 distance: 80 - 81: 41.369 distance: 80 - 82: 45.464 distance: 83 - 84: 16.161 distance: 84 - 85: 10.665 distance: 84 - 87: 12.609 distance: 85 - 94: 53.736 distance: 87 - 88: 8.698 distance: 88 - 89: 16.315 distance: 88 - 90: 14.360 distance: 89 - 91: 26.971 distance: 90 - 92: 12.482 distance: 91 - 93: 10.840 distance: 92 - 93: 21.989 distance: 94 - 95: 24.846 distance: 95 - 96: 25.062 distance: 95 - 98: 20.944 distance: 96 - 97: 31.461 distance: 96 - 100: 26.659 distance: 97 - 122: 48.466 distance: 98 - 99: 49.566 distance: 100 - 101: 5.105 distance: 101 - 102: 21.554 distance: 101 - 104: 45.363 distance: 102 - 103: 38.041 distance: 102 - 105: 28.118 distance: 105 - 106: 35.443 distance: 106 - 107: 28.499 distance: 106 - 109: 41.855 distance: 107 - 108: 6.422 distance: 107 - 113: 6.944 distance: 109 - 110: 18.576 distance: 110 - 111: 21.449 distance: 110 - 112: 30.279 distance: 113 - 114: 15.567 distance: 114 - 115: 5.221 distance: 114 - 117: 45.706 distance: 115 - 116: 10.318 distance: 115 - 122: 48.923 distance: 116 - 145: 22.801 distance: 118 - 119: 20.751 distance: 119 - 120: 29.938 distance: 119 - 121: 29.386 distance: 122 - 123: 13.210 distance: 123 - 124: 12.087 distance: 123 - 126: 27.843 distance: 124 - 125: 9.865 distance: 124 - 130: 20.764 distance: 125 - 154: 27.916 distance: 126 - 127: 19.846 distance: 127 - 128: 29.508 distance: 127 - 129: 17.932 distance: 130 - 131: 15.449 distance: 131 - 132: 16.890 distance: 131 - 134: 22.513 distance: 132 - 135: 28.737 distance: 133 - 165: 30.680 distance: 135 - 136: 18.914 distance: 136 - 137: 31.574 distance: 136 - 139: 17.443 distance: 137 - 138: 13.094 distance: 137 - 145: 18.195 distance: 138 - 172: 21.397 distance: 139 - 140: 23.198 distance: 140 - 141: 14.707 distance: 140 - 142: 19.354 distance: 141 - 143: 11.034 distance: 142 - 144: 10.117 distance: 143 - 144: 8.080 distance: 145 - 146: 16.020 distance: 146 - 147: 20.709 distance: 146 - 149: 37.564 distance: 147 - 148: 3.893 distance: 147 - 154: 29.074 distance: 148 - 177: 29.903 distance: 149 - 150: 31.506 distance: 150 - 151: 15.606 distance: 151 - 152: 11.114 distance: 151 - 153: 32.794