Starting phenix.real_space_refine on Thu Dec 7 17:29:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/12_2023/7wrl_32732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/12_2023/7wrl_32732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/12_2023/7wrl_32732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/12_2023/7wrl_32732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/12_2023/7wrl_32732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrl_32732/12_2023/7wrl_32732.pdb" } resolution = 3.51 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2052 2.51 5 N 548 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 457": "NH1" <-> "NH2" Residue "R GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3251 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 971 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Time building chain proxies: 2.22, per 1000 atoms: 0.68 Number of scatterers: 3251 At special positions: 0 Unit cell: (63.72, 82.08, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 636 8.00 N 548 7.00 C 2052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 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: 1.06 Conformation dependent library (CDL) restraints added in 559.6 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 5.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.969A pdb=" N GLN A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.578A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP R 389 " --> pdb=" O LYS R 386 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 384 through 390' Processing helix chain 'R' and resid 498 through 502 removed outlier: 3.785A pdb=" N TYR R 501 " --> pdb=" O ARG R 498 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY R 502 " --> pdb=" O PRO R 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 498 through 502' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.876A pdb=" N SER A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 50 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 100 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET A 117 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.831A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.537A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.995A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 51 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: 0.71 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1017 1.34 - 1.46: 739 1.46 - 1.57: 1558 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" C ASP A 109 " pdb=" N PHE A 110 " ideal model delta sigma weight residual 1.334 1.305 0.030 1.49e-02 4.50e+03 3.93e+00 bond pdb=" CB CYS B 90 " pdb=" SG CYS B 90 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" C LYS A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.35e+00 bond pdb=" N ALA R 411 " pdb=" CA ALA R 411 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.41e-02 5.03e+03 2.13e+00 bond pdb=" C ALA R 372 " pdb=" N PRO R 373 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 88 106.67 - 113.50: 1690 113.50 - 120.33: 1256 120.33 - 127.16: 1467 127.16 - 133.99: 28 Bond angle restraints: 4529 Sorted by residual: angle pdb=" N VAL R 483 " pdb=" CA VAL R 483 " pdb=" C VAL R 483 " ideal model delta sigma weight residual 106.21 110.82 -4.61 1.07e+00 8.73e-01 1.86e+01 angle pdb=" C GLY R 485 " pdb=" N PHE R 486 " pdb=" CA PHE R 486 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" N VAL R 367 " pdb=" CA VAL R 367 " pdb=" C VAL R 367 " ideal model delta sigma weight residual 112.29 108.61 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" OG1 THR B 94 " pdb=" CB THR B 94 " pdb=" CG2 THR B 94 " ideal model delta sigma weight residual 109.30 102.03 7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C TYR B 51 " pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta sigma weight residual 121.71 116.85 4.86 1.39e+00 5.18e-01 1.22e+01 ... (remaining 4524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1709 17.40 - 34.79: 196 34.79 - 52.19: 33 52.19 - 69.59: 5 69.59 - 86.98: 1 Dihedral angle restraints: 1944 sinusoidal: 734 harmonic: 1210 Sorted by residual: dihedral pdb=" CA LYS A 13 " pdb=" C LYS A 13 " pdb=" N PRO A 14 " pdb=" CA PRO A 14 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG R 466 " pdb=" C ARG R 466 " pdb=" N ASP R 467 " pdb=" CA ASP R 467 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 307 0.047 - 0.094: 120 0.094 - 0.141: 43 0.141 - 0.188: 11 0.188 - 0.235: 4 Chirality restraints: 485 Sorted by residual: chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TYR B 51 " pdb=" N TYR B 51 " pdb=" C TYR B 51 " pdb=" CB TYR B 51 " 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=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.85 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 482 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO R 463 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 338 " -0.014 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE R 338 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE R 338 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE R 338 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE R 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 338 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 338 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 56 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 57 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.031 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 986 2.81 - 3.33: 2686 3.33 - 3.86: 5412 3.86 - 4.38: 6037 4.38 - 4.90: 10870 Nonbonded interactions: 25991 Sorted by model distance: nonbonded pdb=" OG1 THR R 415 " pdb=" OD2 ASP R 420 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR B 32 " pdb=" OD2 ASP R 405 " model vdw 2.312 2.440 nonbonded pdb=" ND2 ASN B 54 " pdb=" O GLY B 66 " model vdw 2.322 2.520 nonbonded pdb=" O SER A 25 " pdb=" OG SER A 25 " model vdw 2.327 2.440 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.327 2.440 ... (remaining 25986 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 9.430 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3332 Z= 0.401 Angle : 1.031 8.952 4529 Z= 0.594 Chirality : 0.060 0.235 485 Planarity : 0.008 0.075 586 Dihedral : 14.713 86.983 1171 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.19 (0.37), residues: 411 helix: -4.93 (0.34), residues: 27 sheet: -2.41 (0.46), residues: 118 loop : -2.86 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 47 HIS 0.002 0.001 HIS B 41 PHE 0.040 0.003 PHE R 338 TYR 0.032 0.003 TYR B 51 ARG 0.023 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1844 time to fit residues: 15.2133 Evaluate side-chains 50 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4968 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 63.4462 > 50: distance: 20 - 167: 20.177 distance: 82 - 88: 14.875 distance: 88 - 89: 12.306 distance: 89 - 90: 11.108 distance: 89 - 92: 9.737 distance: 90 - 91: 7.144 distance: 90 - 100: 16.377 distance: 92 - 93: 18.451 distance: 93 - 94: 18.124 distance: 93 - 95: 11.057 distance: 94 - 96: 4.657 distance: 95 - 97: 19.797 distance: 97 - 98: 16.643 distance: 98 - 99: 12.810 distance: 100 - 101: 17.183 distance: 101 - 102: 31.095 distance: 101 - 104: 17.993 distance: 102 - 103: 26.645 distance: 102 - 109: 32.113 distance: 104 - 105: 25.450 distance: 105 - 106: 25.553 distance: 106 - 107: 16.389 distance: 107 - 108: 14.424 distance: 109 - 110: 21.681 distance: 110 - 111: 44.869 distance: 110 - 113: 40.914 distance: 111 - 117: 7.759 distance: 113 - 114: 5.065 distance: 114 - 115: 45.906 distance: 114 - 116: 34.194 distance: 117 - 123: 40.706 distance: 118 - 119: 25.445 distance: 118 - 121: 12.441 distance: 119 - 120: 21.797 distance: 119 - 124: 9.662 distance: 121 - 122: 28.837 distance: 122 - 123: 50.879 distance: 124 - 125: 18.446 distance: 125 - 126: 22.352 distance: 125 - 128: 23.968 distance: 126 - 127: 27.728 distance: 126 - 132: 13.078 distance: 128 - 129: 16.115 distance: 129 - 130: 8.730 distance: 129 - 131: 15.343 distance: 132 - 133: 12.238 distance: 133 - 134: 18.687 distance: 133 - 136: 28.976 distance: 134 - 135: 35.177 distance: 134 - 140: 11.436 distance: 136 - 137: 20.051 distance: 137 - 138: 25.807 distance: 137 - 139: 25.143 distance: 140 - 141: 31.443 distance: 141 - 142: 10.141 distance: 141 - 144: 25.960 distance: 142 - 143: 8.400 distance: 142 - 151: 20.701 distance: 144 - 145: 23.968 distance: 145 - 146: 23.456 distance: 145 - 147: 26.277 distance: 146 - 148: 32.109 distance: 147 - 149: 28.449 distance: 148 - 150: 18.123 distance: 149 - 150: 16.267 distance: 151 - 152: 38.478 distance: 152 - 153: 19.761 distance: 152 - 155: 26.770 distance: 153 - 154: 19.885 distance: 153 - 158: 9.915 distance: 155 - 156: 12.767 distance: 155 - 157: 53.732 distance: 158 - 159: 22.321 distance: 159 - 160: 15.996 distance: 160 - 161: 7.552 distance: 160 - 162: 5.402 distance: 162 - 163: 19.150 distance: 162 - 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