Starting phenix.real_space_refine on Tue Mar 11 17:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7phg_13415/03_2025/7phg_13415_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phg_13415/03_2025/7phg_13415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2025/7phg_13415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2025/7phg_13415.map" model { file = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2025/7phg_13415_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phg_13415/03_2025/7phg_13415_neut.cif" } resolution = 4.3 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= 1.000 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 2093 2.51 5 N 558 2.21 5 O 640 1.98 5 H 3160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6469 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3022 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1819 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1628 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Time building chain proxies: 6.19, per 1000 atoms: 0.96 Number of scatterers: 6469 At special positions: 0 Unit cell: (72.98, 52.48, 100.04, 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 640 8.00 N 558 7.00 C 2093 6.00 H 3160 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 1.65 Conformation dependent library (CDL) restraints added in 616.9 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.790A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.989A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.115A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.762A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.108A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP H 50 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.524A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 159 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: 2.17 Time building geometry restraints manager: 2.04 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: 3160 1.03 - 1.23: 4 1.23 - 1.42: 1500 1.42 - 1.62: 1866 1.62 - 1.82: 22 Bond restraints: 6552 Sorted by residual: bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.76e+00 bond pdb=" CA VAL A 524 " pdb=" CB VAL A 524 " ideal model delta sigma weight residual 1.530 1.542 -0.013 1.11e-02 8.12e+03 1.30e+00 bond pdb=" C PHE H 29 " pdb=" N THR H 30 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.07e+00 bond pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.63e-01 bond pdb=" CA ILE H 48 " pdb=" CB ILE H 48 " ideal model delta sigma weight residual 1.545 1.532 0.013 1.45e-02 4.76e+03 8.24e-01 ... (remaining 6547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11425 1.47 - 2.94: 273 2.94 - 4.40: 38 4.40 - 5.87: 5 5.87 - 7.34: 2 Bond angle restraints: 11743 Sorted by residual: angle pdb=" N ILE H 48 " pdb=" CA ILE H 48 " pdb=" C ILE H 48 " ideal model delta sigma weight residual 111.62 104.28 7.34 7.90e-01 1.60e+00 8.63e+01 angle pdb=" N TRP H 47 " pdb=" CA TRP H 47 " pdb=" C TRP H 47 " ideal model delta sigma weight residual 110.24 116.38 -6.14 1.30e+00 5.92e-01 2.23e+01 angle pdb=" N GLY A 381 " pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 113.58 109.75 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" C TRP H 47 " pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " ideal model delta sigma weight residual 109.64 104.40 5.24 1.77e+00 3.19e-01 8.76e+00 angle pdb=" C PRO A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 ... (remaining 11738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2777 16.08 - 32.15: 262 32.15 - 48.22: 80 48.22 - 64.30: 37 64.30 - 80.37: 8 Dihedral angle restraints: 3164 sinusoidal: 1677 harmonic: 1487 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 28.65 64.35 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -143.11 57.11 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS H 97 " pdb=" SG CYS H 97 " pdb=" SG CYS H 100B" pdb=" CB CYS H 100B" ideal model delta sinusoidal sigma weight residual -86.00 -45.36 -40.64 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 349 0.042 - 0.083: 101 0.083 - 0.125: 36 0.125 - 0.167: 5 0.167 - 0.209: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE H 48 " pdb=" N ILE H 48 " pdb=" C ILE H 48 " pdb=" CB ILE H 48 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TRP H 47 " pdb=" N TRP H 47 " pdb=" C TRP H 47 " pdb=" CB TRP H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" C PRO L 80 " pdb=" CB PRO L 80 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 489 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.022 2.00e-02 2.50e+03 1.06e-02 4.46e+00 pdb=" CG TRP H 47 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP H 47 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO L 95 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 35 " 0.009 2.00e-02 2.50e+03 7.85e-03 2.46e+00 pdb=" CG TRP L 35 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP L 35 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 35 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP L 35 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP L 35 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP L 35 " 0.002 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 210 2.10 - 2.72: 11442 2.72 - 3.35: 18874 3.35 - 3.97: 24223 3.97 - 4.60: 37018 Nonbonded interactions: 91767 Sorted by model distance: nonbonded pdb=" H TYR A 453 " pdb=" O GLN A 493 " model vdw 1.473 2.450 nonbonded pdb="HH22 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 1.594 2.450 nonbonded pdb=" H GLN A 498 " pdb=" OD1 ASN A 501 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLN H 6 " pdb=" H GLY H 106 " model vdw 1.608 2.450 nonbonded pdb=" O SER L 76 " pdb=" HE ARG L 77 " model vdw 1.641 2.450 ... (remaining 91762 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 ========== 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: 10.540 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: 0.040 Set scattering table: 0.060 Process input model: 21.270 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.003 0.041 3392 Z= 0.208 Angle : 0.677 7.339 4608 Z= 0.402 Chirality : 0.045 0.209 492 Planarity : 0.005 0.046 599 Dihedral : 13.712 80.375 1206 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.68 (0.37), residues: 421 helix: -4.42 (0.50), residues: 19 sheet: -2.65 (0.38), residues: 124 loop : -2.28 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.017 0.002 PHE A 347 TYR 0.027 0.002 TYR L 87 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7500 (tmm160) cc_final: 0.7146 (tmt170) REVERT: A 351 TYR cc_start: 0.7985 (p90) cc_final: 0.7743 (p90) REVERT: A 394 ASN cc_start: 0.8238 (m110) cc_final: 0.7884 (m110) REVERT: A 512 VAL cc_start: 0.8767 (t) cc_final: 0.8529 (t) REVERT: H 2 MET cc_start: 0.5821 (mmp) cc_final: 0.5591 (mmp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3881 time to fit residues: 38.8509 Evaluate side-chains 70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3178 > 50: distance: 206 - 218: 6.372 distance: 218 - 219: 6.987 distance: 218 - 230: 11.197 distance: 219 - 220: 3.983 distance: 219 - 222: 7.794 distance: 219 - 231: 14.794 distance: 220 - 221: 6.370 distance: 220 - 239: 12.014 distance: 222 - 232: 10.327 distance: 222 - 233: 6.057 distance: 223 - 224: 6.111 distance: 223 - 225: 10.525 distance: 224 - 226: 13.675 distance: 224 - 234: 5.276 distance: 225 - 227: 8.273 distance: 225 - 235: 3.679 distance: 226 - 228: 6.569 distance: 226 - 236: 9.536 distance: 227 - 228: 10.685 distance: 227 - 237: 5.217 distance: 228 - 229: 6.653 distance: 229 - 238: 16.071 distance: 239 - 240: 13.907 distance: 239 - 247: 12.092 distance: 240 - 241: 3.199 distance: 240 - 243: 16.353 distance: 240 - 248: 9.876 distance: 241 - 242: 6.890 distance: 241 - 258: 15.210 distance: 243 - 244: 18.849 distance: 243 - 249: 22.343 distance: 243 - 250: 18.400 distance: 244 - 245: 20.750 distance: 244 - 246: 19.871 distance: 244 - 251: 5.212 distance: 245 - 252: 13.027 distance: 245 - 253: 25.178 distance: 245 - 254: 19.347 distance: 246 - 255: 13.366 distance: 246 - 256: 11.380 distance: 246 - 257: 21.268 distance: 258 - 259: 8.123 distance: 259 - 260: 9.649 distance: 259 - 262: 4.255 distance: 259 - 271: 25.540 distance: 260 - 261: 7.139 distance: 260 - 279: 9.067 distance: 262 - 263: 7.894 distance: 262 - 272: 28.113 distance: 262 - 273: 12.477 distance: 263 - 264: 6.136 distance: 263 - 265: 3.726 distance: 264 - 266: 11.624 distance: 264 - 274: 10.932 distance: 265 - 267: 8.218 distance: 265 - 275: 8.671 distance: 266 - 268: 5.132 distance: 266 - 276: 4.478 distance: 267 - 268: 5.843 distance: 267 - 277: 3.870 distance: 268 - 269: 5.443 distance: 269 - 278: 9.863 distance: 279 - 280: 7.210 distance: 279 - 290: 9.066 distance: 280 - 281: 5.095 distance: 280 - 283: 10.203 distance: 280 - 291: 4.375 distance: 281 - 282: 11.300 distance: 281 - 303: 7.387 distance: 283 - 284: 20.496 distance: 283 - 292: 8.589 distance: 283 - 293: 14.274 distance: 284 - 285: 16.987 distance: 284 - 294: 53.318 distance: 284 - 295: 36.268 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