Starting phenix.real_space_refine on Sat Aug 3 04:34:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/08_2024/8ubw_42107_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/08_2024/8ubw_42107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/08_2024/8ubw_42107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/08_2024/8ubw_42107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/08_2024/8ubw_42107_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/08_2024/8ubw_42107_trim.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.025 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 S 18 5.16 5 C 2259 2.51 5 N 502 2.21 5 O 619 1.98 5 H 3343 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6741 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 6591 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 150 Unusual residues: {'CHT': 1, 'Y01': 3} Classifications: {'undetermined': 4, 'water': 38} Link IDs: {None: 41} Time building chain proxies: 4.57, per 1000 atoms: 0.68 Number of scatterers: 6741 At special positions: 0 Unit cell: (84.1, 55.1, 65.975, 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 18 16.00 O 619 8.00 N 502 7.00 C 2259 6.00 H 3343 1.00 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 - 3.50 Amino acid : False - 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: 7.60 Conformation dependent library (CDL) restraints added in 696.4 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.981A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.730A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.021A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.870A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 removed outlier: 3.649A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.244A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.512A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.147A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 397 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 454 removed outlier: 3.500A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 488 removed outlier: 3.516A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.868A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 2.41 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3335 1.03 - 1.23: 11 1.23 - 1.42: 1394 1.42 - 1.62: 2026 1.62 - 1.81: 28 Bond restraints: 6794 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.01e+00 bond pdb=" CB ASN A 265 " pdb=" CG ASN A 265 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.57e-01 bond pdb=" C VAL A 260 " pdb=" O VAL A 260 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.33e-01 bond pdb=" N VAL A 260 " pdb=" CA VAL A 260 " ideal model delta sigma weight residual 1.456 1.462 -0.006 8.60e-03 1.35e+04 4.35e-01 bond pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 3.86e-01 ... (remaining 6789 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 112 106.71 - 113.52: 7993 113.52 - 120.33: 2307 120.33 - 127.14: 1822 127.14 - 133.96: 36 Bond angle restraints: 12270 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 106.21 109.73 -3.52 1.07e+00 8.73e-01 1.08e+01 angle pdb=" C ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 114.00 110.64 3.36 1.31e+00 5.83e-01 6.57e+00 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.33 122.28 -1.95 8.00e-01 1.56e+00 5.95e+00 angle pdb=" C VAL A 195 " pdb=" CA VAL A 195 " pdb=" CB VAL A 195 " ideal model delta sigma weight residual 113.22 110.82 2.40 1.12e+00 7.97e-01 4.60e+00 angle pdb=" CA VAL A 195 " pdb=" C VAL A 195 " pdb=" O VAL A 195 " ideal model delta sigma weight residual 122.63 120.87 1.76 8.70e-01 1.32e+00 4.08e+00 ... (remaining 12265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3034 17.95 - 35.91: 200 35.91 - 53.86: 100 53.86 - 71.82: 29 71.82 - 89.77: 3 Dihedral angle restraints: 3366 sinusoidal: 1889 harmonic: 1477 Sorted by residual: dihedral pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N LEU A 255 " pdb=" CA LEU A 255 " ideal model delta harmonic sigma weight residual 180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB MET A 358 " pdb=" CG MET A 358 " pdb=" SD MET A 358 " pdb=" CE MET A 358 " ideal model delta sinusoidal sigma weight residual 60.00 5.96 54.04 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " pdb=" CG ARG A 372 " pdb=" CD ARG A 372 " ideal model delta sinusoidal sigma weight residual -180.00 -129.13 -50.87 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 3363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 374 0.023 - 0.045: 103 0.045 - 0.067: 44 0.067 - 0.090: 38 0.090 - 0.112: 9 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ASN A 331 " pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CB ASN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 565 not shown) Planarity restraints: 957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 114 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE A 114 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 114 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 230 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 231 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.005 2.00e-02 2.50e+03 9.06e-03 1.23e+00 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 331 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 331 " -0.001 2.00e-02 2.50e+03 ... (remaining 954 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 931 2.26 - 2.85: 15618 2.85 - 3.43: 18994 3.43 - 4.02: 25823 4.02 - 4.60: 39249 Nonbonded interactions: 100615 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" HG1 THR A 419 " model vdw 1.679 2.450 nonbonded pdb=" HG SER A 350 " pdb=" OE1 GLN A 481 " model vdw 1.699 2.450 nonbonded pdb=" HH TYR A 349 " pdb=" O HOH A 702 " model vdw 1.736 2.450 nonbonded pdb=" HH TYR A 139 " pdb=" O SER A 194 " model vdw 1.750 2.450 nonbonded pdb=" H GLY A 219 " pdb=" O HOH A 707 " model vdw 1.762 2.450 ... (remaining 100610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 28.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.002 0.022 3451 Z= 0.133 Angle : 0.476 4.974 4724 Z= 0.269 Chirality : 0.033 0.112 568 Planarity : 0.003 0.029 557 Dihedral : 14.624 89.769 1369 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.85 % Allowed : 14.41 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.42), residues: 416 helix: 3.09 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.68 (0.55), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.015 0.001 TYR A 117 ARG 0.005 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.7974 (m-80) cc_final: 0.7672 (m-80) REVERT: A 459 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6840 (tm-30) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 2.2949 time to fit residues: 109.2697 Evaluate side-chains 34 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1308 > 50: distance: 152 - 165: 3.170 distance: 165 - 166: 3.187 distance: 165 - 173: 7.110 distance: 166 - 167: 3.580 distance: 167 - 184: 4.355 distance: 169 - 170: 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225: 7.138 distance: 224 - 230: 18.346 distance: 225 - 226: 4.845 distance: 225 - 228: 8.643 distance: 225 - 231: 4.292 distance: 226 - 227: 6.665 distance: 226 - 235: 4.898 distance: 227 - 288: 13.787 distance: 228 - 229: 13.380 distance: 228 - 232: 6.891 distance: 229 - 234: 11.710 distance: 235 - 236: 4.602 distance: 236 - 237: 5.714 distance: 236 - 239: 3.332 distance: 236 - 247: 3.241 distance: 237 - 238: 4.175 distance: 237 - 259: 4.645 distance: 238 - 299: 10.096 distance: 239 - 240: 5.266 distance: 240 - 241: 3.700 distance: 240 - 250: 3.724 distance: 240 - 251: 5.643 distance: 241 - 252: 3.996 distance: 259 - 260: 3.836 distance: 260 - 261: 3.051 distance: 261 - 262: 3.607 distance: 262 - 315: 4.977 distance: 263 - 264: 4.842 distance: 263 - 265: 5.091 distance: 263 - 269: 4.863 distance: 264 - 270: 3.306 distance: 264 - 271: 4.822 distance: 266 - 275: 3.258 distance: 266 - 277: 3.202 distance: 278 - 279: 6.048 distance: 278 - 283: 3.704 distance: 279 - 280: 7.143 distance: 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