Starting phenix.real_space_refine on Mon Jun 24 13:20:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/06_2024/8x64_38079_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/06_2024/8x64_38079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/06_2024/8x64_38079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/06_2024/8x64_38079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/06_2024/8x64_38079_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x64_38079/06_2024/8x64_38079_updated.pdb" } resolution = 3.4 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= -0.001 sd= 0.056 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 20 5.16 5 Cl 1 4.86 5 C 1472 2.51 5 N 351 2.21 5 O 345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 2189 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2167 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y5R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 1.02 Number of scatterers: 2189 At special positions: 0 Unit cell: (54.06, 73.14, 71.02, 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) Cl 1 17.00 S 20 16.00 O 345 8.00 N 351 7.00 C 1472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " 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: 0.81 Conformation dependent library (CDL) restraints added in 369.8 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 28 through 52 removed outlier: 3.669A pdb=" N CYS B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 89 removed outlier: 3.686A pdb=" N LEU B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 129 removed outlier: 3.825A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 164 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 188 through 219 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 438 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 448 through 471 removed outlier: 3.516A pdb=" N PHE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 473 through 480 removed outlier: 3.591A pdb=" N LYS B 476 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 477 " --> pdb=" O ASN B 474 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 478 " --> pdb=" O PHE B 475 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 423 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: 0.50 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 305 1.30 - 1.43: 644 1.43 - 1.56: 1268 1.56 - 1.68: 2 1.68 - 1.81: 32 Bond restraints: 2251 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.332 1.257 0.075 1.36e-02 5.41e+03 3.04e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.235 1.172 0.064 1.26e-02 6.30e+03 2.55e+01 bond pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta sigma weight residual 1.530 1.447 0.084 1.69e-02 3.50e+03 2.44e+01 bond pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.32e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.396 0.061 1.29e-02 6.01e+03 2.27e+01 ... (remaining 2246 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.27: 59 106.27 - 113.20: 1220 113.20 - 120.13: 839 120.13 - 127.07: 906 127.07 - 134.00: 30 Bond angle restraints: 3054 Sorted by residual: angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.30 124.60 -7.30 1.16e+00 7.43e-01 3.96e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.12 116.20 5.92 1.06e+00 8.90e-01 3.12e+01 angle pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" C PHE B 424 " ideal model delta sigma weight residual 110.80 102.52 8.28 2.13e+00 2.20e-01 1.51e+01 angle pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " ideal model delta sigma weight residual 116.60 121.79 -5.19 1.45e+00 4.76e-01 1.28e+01 angle pdb=" N ALA B 423 " pdb=" CA ALA B 423 " pdb=" C ALA B 423 " ideal model delta sigma weight residual 111.28 114.76 -3.48 1.09e+00 8.42e-01 1.02e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 1116 14.25 - 28.50: 145 28.50 - 42.74: 52 42.74 - 56.99: 7 56.99 - 71.24: 1 Dihedral angle restraints: 1321 sinusoidal: 538 harmonic: 783 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -142.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" C ILE B 115 " pdb=" N ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual -122.00 -134.73 12.73 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta harmonic sigma weight residual 123.40 135.77 -12.37 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 328 0.085 - 0.169: 20 0.169 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.423: 1 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA MET B 81 " pdb=" N MET B 81 " pdb=" C MET B 81 " pdb=" CB MET B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CB ILE B 115 " pdb=" CA ILE B 115 " pdb=" CG1 ILE B 115 " pdb=" CG2 ILE B 115 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 346 not shown) Planarity restraints: 358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PHE B 424 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE B 424 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 425 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C SER B 114 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 78 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ALA B 78 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA B 78 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 79 " -0.015 2.00e-02 2.50e+03 ... (remaining 355 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 609 2.81 - 3.33: 2236 3.33 - 3.86: 3468 3.86 - 4.38: 3790 4.38 - 4.90: 6262 Nonbonded interactions: 16365 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP B 73 " pdb=" OG SER B 461 " model vdw 2.296 2.440 nonbonded pdb=" O PHE B 424 " pdb=" C ILE B 425 " model vdw 2.317 3.270 nonbonded pdb=" O ALA B 423 " pdb=" ND2 ASN B 460 " model vdw 2.380 2.520 nonbonded pdb=" OH TYR B 214 " pdb=" NZ LYS B 218 " model vdw 2.384 2.520 ... (remaining 16360 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=0.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.490 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 0.084 2251 Z= 0.413 Angle : 0.789 8.277 3054 Z= 0.428 Chirality : 0.048 0.423 349 Planarity : 0.007 0.047 358 Dihedral : 14.113 71.238 805 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.42 % Allowed : 0.00 % Favored : 99.58 % Cbeta Deviations : 0.39 % 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: -0.76 (0.53), residues: 255 helix: 0.47 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -3.69 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 455 HIS 0.003 0.001 HIS B 450 PHE 0.010 0.001 PHE B 435 TYR 0.018 0.001 TYR B 200 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.246 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1370 time to fit residues: 7.0469 Evaluate side-chains 36 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2251 Z= 0.257 Angle : 0.704 7.437 3054 Z= 0.355 Chirality : 0.042 0.135 349 Planarity : 0.006 0.044 358 Dihedral : 5.848 52.212 299 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.93 % Allowed : 14.23 % Favored : 82.85 % 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: -0.51 (0.52), residues: 255 helix: 0.69 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -3.75 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.012 0.001 PHE B 435 TYR 0.010 0.002 TYR B 126 ARG 0.001 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 206 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.4253 (ttm) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.1439 time to fit residues: 6.0712 Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4987 > 50: distance: 60 - 67: 9.339 distance: 67 - 68: 18.662 distance: 68 - 69: 42.686 distance: 68 - 71: 5.747 distance: 69 - 70: 43.542 distance: 69 - 77: 40.101 distance: 71 - 72: 23.465 distance: 72 - 73: 39.090 distance: 72 - 74: 40.251 distance: 73 - 75: 40.853 distance: 74 - 76: 42.540 distance: 75 - 76: 38.105 distance: 77 - 78: 60.919 distance: 78 - 79: 34.846 distance: 78 - 81: 53.289 distance: 79 - 80: 28.211 distance: 79 - 85: 27.804 distance: 81 - 82: 14.283 distance: 82 - 83: 7.016 distance: 82 - 84: 11.243 distance: 85 - 86: 40.270 distance: 86 - 87: 36.420 distance: 86 - 89: 25.277 distance: 87 - 88: 45.632 distance: 87 - 95: 5.754 distance: 88 - 121: 12.513 distance: 89 - 90: 17.799 distance: 90 - 91: 37.203 distance: 90 - 92: 9.094 distance: 91 - 93: 27.326 distance: 92 - 94: 42.212 distance: 93 - 94: 17.609 distance: 95 - 96: 9.047 distance: 96 - 97: 38.152 distance: 96 - 99: 20.317 distance: 97 - 98: 20.444 distance: 97 - 103: 42.252 distance: 98 - 129: 44.189 distance: 99 - 100: 10.839 distance: 100 - 101: 6.092 distance: 101 - 102: 11.828 distance: 103 - 104: 18.650 distance: 104 - 105: 25.055 distance: 104 - 107: 15.821 distance: 105 - 106: 28.510 distance: 105 - 114: 13.211 distance: 107 - 108: 8.750 distance: 108 - 109: 9.931 distance: 108 - 110: 13.417 distance: 109 - 111: 5.415 distance: 111 - 113: 3.924 distance: 114 - 115: 15.995 distance: 115 - 116: 12.206 distance: 115 - 118: 12.512 distance: 116 - 117: 19.514 distance: 116 - 121: 30.583 distance: 117 - 151: 32.320 distance: 118 - 119: 14.714 distance: 118 - 120: 6.330 distance: 121 - 122: 60.677 distance: 122 - 123: 40.222 distance: 122 - 125: 63.559 distance: 123 - 124: 43.266 distance: 123 - 129: 28.839 distance: 124 - 155: 34.998 distance: 125 - 126: 36.631 distance: 125 - 127: 47.622 distance: 126 - 128: 12.926 distance: 129 - 130: 26.129 distance: 130 - 131: 7.770 distance: 130 - 133: 3.975 distance: 131 - 132: 26.568 distance: 131 - 143: 10.367 distance: 132 - 167: 9.867 distance: 133 - 134: 16.836 distance: 134 - 135: 9.595 distance: 134 - 136: 11.099 distance: 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