Starting phenix.real_space_refine on Fri Aug 2 12:49:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/08_2024/6rju_4906.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/08_2024/6rju_4906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/08_2024/6rju_4906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/08_2024/6rju_4906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/08_2024/6rju_4906.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/08_2024/6rju_4906.cif" } resolution = 3.2 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= 0.002 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: 6 Type Number sf(0) Gaussians Se 3 7.20 5 S 1 5.16 5 C 625 2.51 5 N 178 2.21 5 O 188 1.98 5 H 997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A GLU 509": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 1992 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1992 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.83, per 1000 atoms: 0.92 Number of scatterers: 1992 At special positions: 0 Unit cell: (57.132, 40.204, 83.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 3 33.99 S 1 16.00 O 188 8.00 N 178 7.00 C 625 6.00 H 997 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: 0.94 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 254 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 72.5% 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 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.613A pdb=" N ASP A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 removed outlier: 3.590A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 4.511A pdb=" N ARG A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 4.019A pdb=" N HIS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 494 removed outlier: 3.674A pdb=" N VAL A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MSE A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 510 through 517 removed outlier: 4.037A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.626A pdb=" N ALA A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 525 " --> pdb=" O ARG A 522 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 117 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: 0.41 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 996 1.06 - 1.29: 177 1.29 - 1.51: 452 1.51 - 1.73: 372 1.73 - 1.96: 7 Bond restraints: 2004 Sorted by residual: bond pdb=" CB ASN A 452 " pdb=" CG ASN A 452 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.90e+00 bond pdb=" CG GLU A 461 " pdb=" CD GLU A 461 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.99e+00 bond pdb=" CB GLU A 461 " pdb=" CG GLU A 461 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " ideal model delta sigma weight residual 1.532 1.553 -0.021 1.51e-02 4.39e+03 1.90e+00 bond pdb=" CB TRP A 474 " pdb=" CG TRP A 474 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.61e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.39: 26 105.39 - 112.56: 2388 112.56 - 119.72: 552 119.72 - 126.89: 657 126.89 - 134.06: 15 Bond angle restraints: 3638 Sorted by residual: angle pdb=" C LYS A 451 " pdb=" N ASN A 452 " pdb=" CA ASN A 452 " ideal model delta sigma weight residual 122.61 128.50 -5.89 1.56e+00 4.11e-01 1.42e+01 angle pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " pdb=" CG ASN A 452 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" CA GLN A 505 " pdb=" C GLN A 505 " pdb=" N PRO A 506 " ideal model delta sigma weight residual 118.44 122.27 -3.83 1.59e+00 3.96e-01 5.82e+00 angle pdb=" N ASN A 452 " pdb=" CA ASN A 452 " pdb=" C ASN A 452 " ideal model delta sigma weight residual 112.47 115.25 -2.78 1.24e+00 6.50e-01 5.04e+00 angle pdb=" N ARG A 468 " pdb=" CA ARG A 468 " pdb=" C ARG A 468 " ideal model delta sigma weight residual 108.23 105.14 3.09 1.38e+00 5.25e-01 5.02e+00 ... (remaining 3633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 817 16.29 - 32.59: 73 32.59 - 48.88: 19 48.88 - 65.17: 11 65.17 - 81.47: 2 Dihedral angle restraints: 922 sinusoidal: 509 harmonic: 413 Sorted by residual: dihedral pdb=" CA LEU A 469 " pdb=" C LEU A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA THR A 470 " pdb=" C THR A 470 " pdb=" N LEU A 471 " pdb=" CA LEU A 471 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR A 449 " pdb=" C THR A 449 " pdb=" N GLY A 450 " pdb=" CA GLY A 450 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 111 0.046 - 0.092: 46 0.092 - 0.137: 7 0.137 - 0.183: 0 0.183 - 0.229: 1 Chirality restraints: 165 Sorted by residual: chirality pdb=" CA ASN A 452 " pdb=" N ASN A 452 " pdb=" C ASN A 452 " pdb=" CB ASN A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLN A 505 " pdb=" N GLN A 505 " pdb=" C GLN A 505 " pdb=" CB GLN A 505 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ASN A 413 " pdb=" N ASN A 413 " pdb=" C ASN A 413 " pdb=" CB ASN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.17e-01 ... (remaining 162 not shown) Planarity restraints: 302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 505 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 506 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 451 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C LYS A 451 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS A 451 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 452 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " -0.002 2.00e-02 2.50e+03 6.48e-03 1.68e+00 pdb=" CG TRP A 474 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 474 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 474 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 474 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 474 " -0.002 2.00e-02 2.50e+03 ... (remaining 299 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.33: 400 2.33 - 2.94: 4685 2.94 - 3.56: 4919 3.56 - 4.18: 6409 4.18 - 4.80: 9891 Nonbonded interactions: 26304 Sorted by model distance: nonbonded pdb=" H VAL A 502 " pdb="HG22 VAL A 502 " model vdw 1.708 2.270 nonbonded pdb=" HA ARG A 468 " pdb=" HD2 ARG A 468 " model vdw 1.721 2.440 nonbonded pdb=" OG SER A 494 " pdb=" H ALA A 495 " model vdw 1.776 2.450 nonbonded pdb=" O THR A 497 " pdb=" HG1 THR A 497 " model vdw 1.783 2.450 nonbonded pdb=" H ILE A 516 " pdb="HG13 ILE A 516 " model vdw 1.796 2.270 ... (remaining 26299 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: 1.330 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0287 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 : 0.007 0.049 1007 Z= 0.437 Angle : 0.929 6.431 1366 Z= 0.516 Chirality : 0.049 0.229 165 Planarity : 0.005 0.047 176 Dihedral : 15.358 81.468 373 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -7.10 (0.41), residues: 129 helix: -4.88 (0.19), residues: 79 sheet: None (None), residues: 0 loop : -4.14 (0.69), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 474 HIS 0.003 0.001 HIS A 457 PHE 0.011 0.004 PHE A 480 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 13 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.5497 time to fit residues: 7.5550 Evaluate side-chains 8 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 69.1164 > 50: distance: 30 - 42: 15.378 distance: 42 - 43: 30.174 distance: 42 - 46: 22.673 distance: 43 - 44: 16.545 distance: 43 - 47: 28.668 distance: 43 - 48: 41.690 distance: 44 - 45: 13.575 distance: 44 - 49: 16.296 distance: 49 - 50: 14.916 distance: 49 - 57: 4.374 distance: 50 - 51: 8.410 distance: 50 - 58: 15.224 distance: 51 - 52: 34.108 distance: 51 - 68: 19.787 distance: 53 - 54: 18.626 distance: 53 - 55: 40.814 distance: 53 - 59: 21.733 distance: 54 - 56: 20.913 distance: 54 - 60: 11.000 distance: 55 - 62: 10.217 distance: 55 - 63: 33.402 distance: 55 - 64: 24.422 distance: 56 - 66: 10.965 distance: 56 - 67: 6.143 distance: 68 - 69: 26.102 distance: 68 - 77: 3.468 distance: 69 - 70: 14.626 distance: 69 - 72: 28.230 distance: 69 - 78: 18.055 distance: 70 - 71: 15.690 distance: 70 - 85: 38.071 distance: 72 - 73: 43.641 distance: 72 - 79: 43.209 distance: 72 - 80: 58.676 distance: 73 - 74: 29.355 distance: 73 - 81: 26.906 distance: 73 - 82: 15.846 distance: 74 - 75: 12.979 distance: 74 - 76: 7.695 distance: 76 - 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