Starting phenix.real_space_refine on Thu Dec 7 18:57:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/12_2023/7zr8_14886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/12_2023/7zr8_14886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/12_2023/7zr8_14886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/12_2023/7zr8_14886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/12_2023/7zr8_14886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/12_2023/7zr8_14886.pdb" } resolution = 3.7 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= 0.012 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 18 5.16 5 C 2346 2.51 5 N 623 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3693 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 13, 'TRANS': 231} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.58, per 1000 atoms: 0.70 Number of scatterers: 3693 At special positions: 0 Unit cell: (68.06, 75.53, 111.22, 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 18 16.00 O 706 8.00 N 623 7.00 C 2346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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 - 3.50 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 340 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 800.2 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 866 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 9.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.601A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.017A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.371A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.137A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.569A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.794A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.530A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.339A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 252 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: 1.03 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1178 1.34 - 1.46: 930 1.46 - 1.58: 1653 1.58 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 3784 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.08e-01 bond pdb=" C4 NAG A1301 " pdb=" O4 NAG A1301 " ideal model delta sigma weight residual 1.409 1.423 -0.014 2.00e-02 2.50e+03 4.82e-01 ... (remaining 3779 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.02: 106 107.02 - 113.77: 2016 113.77 - 120.51: 1398 120.51 - 127.26: 1583 127.26 - 134.01: 34 Bond angle restraints: 5137 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.77 109.00 2.77 1.04e+00 9.25e-01 7.10e+00 angle pdb=" C ALA A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 121.65 119.16 2.49 1.01e+00 9.80e-01 6.07e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" CB ASP H 103 " ideal model delta sigma weight residual 113.65 110.44 3.21 1.47e+00 4.63e-01 4.78e+00 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 112.97 110.97 2.00 1.06e+00 8.90e-01 3.57e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.02 -3.48 1.91e+00 2.74e-01 3.32e+00 ... (remaining 5132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.18: 2044 10.18 - 20.36: 146 20.36 - 30.54: 47 30.54 - 40.72: 13 40.72 - 50.90: 5 Dihedral angle restraints: 2255 sinusoidal: 893 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 129.10 50.90 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA PRO A 524 " pdb=" C PRO A 524 " pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" N TYR A 498 " pdb=" CA TYR A 498 " pdb=" CB TYR A 498 " pdb=" CG TYR A 498 " ideal model delta sinusoidal sigma weight residual -60.00 -108.10 48.10 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 2252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 340 0.030 - 0.059: 142 0.059 - 0.089: 30 0.089 - 0.118: 42 0.118 - 0.148: 4 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 399 " pdb=" N ILE A 399 " pdb=" C ILE A 399 " pdb=" CB ILE A 399 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 555 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO L 96 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 326 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 327 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 558 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.014 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 174 2.73 - 3.27: 3512 3.27 - 3.81: 5835 3.81 - 4.36: 7174 4.36 - 4.90: 12818 Nonbonded interactions: 29513 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.181 2.440 nonbonded pdb=" OG1 THR H 33 " pdb=" OG SER H 99 " model vdw 2.223 2.440 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.255 2.440 nonbonded pdb=" O LYS H 13 " pdb=" OG SER H 16 " model vdw 2.281 2.440 nonbonded pdb=" O GLN L 90 " pdb=" N GLU L 92 " model vdw 2.291 2.520 ... (remaining 29508 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: 4.230 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: 14.620 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.230 Find NCS groups from input model: 0.110 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 0.028 3784 Z= 0.175 Angle : 0.465 5.767 5137 Z= 0.249 Chirality : 0.042 0.148 558 Planarity : 0.004 0.049 663 Dihedral : 8.421 50.903 1371 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.74 % Allowed : 3.71 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.94 (0.42), residues: 465 helix: -3.12 (0.74), residues: 33 sheet: -0.75 (0.46), residues: 156 loop : -0.08 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 516 PHE 0.009 0.001 PHE A 426 TYR 0.009 0.001 TYR L 91 ARG 0.001 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.2112 time to fit residues: 22.2859 Evaluate side-chains 65 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0456 time to fit residues: 0.7665 ------------------------------------------------------------------------------- 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: 64.9758 > 50: distance: 25 - 47: 3.271 distance: 68 - 72: 12.234 distance: 72 - 73: 18.868 distance: 73 - 74: 17.375 distance: 73 - 76: 19.690 distance: 74 - 75: 16.615 distance: 74 - 80: 34.019 distance: 76 - 77: 31.880 distance: 77 - 78: 19.583 distance: 77 - 79: 24.705 distance: 80 - 81: 21.355 distance: 80 - 230: 23.182 distance: 81 - 82: 21.322 distance: 81 - 84: 12.222 distance: 82 - 83: 9.051 distance: 82 - 92: 22.398 distance: 83 - 227: 27.139 distance: 84 - 85: 11.929 distance: 85 - 86: 28.635 distance: 85 - 87: 10.591 distance: 86 - 88: 17.926 distance: 87 - 89: 11.396 distance: 88 - 90: 22.754 distance: 89 - 90: 12.459 distance: 90 - 91: 11.004 distance: 92 - 93: 25.310 distance: 93 - 94: 23.754 distance: 93 - 96: 17.773 distance: 94 - 95: 25.900 distance: 94 - 103: 35.084 distance: 96 - 97: 32.033 distance: 97 - 98: 25.214 distance: 98 - 99: 17.676 distance: 99 - 100: 8.041 distance: 100 - 101: 19.412 distance: 100 - 102: 19.924 distance: 103 - 104: 9.956 distance: 104 - 105: 38.704 distance: 104 - 107: 27.862 distance: 105 - 106: 27.478 distance: 105 - 111: 16.619 distance: 107 - 108: 35.768 distance: 108 - 109: 22.386 distance: 108 - 110: 27.472 distance: 111 - 112: 9.523 distance: 112 - 113: 13.373 distance: 112 - 115: 17.290 distance: 113 - 114: 16.072 distance: 113 - 122: 8.086 distance: 115 - 116: 19.078 distance: 116 - 117: 13.819 distance: 116 - 118: 29.147 distance: 117 - 119: 20.788 distance: 118 - 120: 14.565 distance: 119 - 121: 7.177 distance: 120 - 121: 31.650 distance: 122 - 123: 13.777 distance: 123 - 124: 20.703 distance: 123 - 126: 22.772 distance: 124 - 125: 11.516 distance: 124 - 133: 14.487 distance: 126 - 127: 15.959 distance: 127 - 128: 7.723 distance: 128 - 129: 12.412 distance: 129 - 130: 8.671 distance: 130 - 131: 4.868 distance: 130 - 132: 12.320 distance: 133 - 134: 10.243 distance: 134 - 135: 15.871 distance: 134 - 137: 19.774 distance: 135 - 136: 3.707 distance: 135 - 142: 13.256 distance: 137 - 138: 34.069 distance: 138 - 139: 25.798 distance: 139 - 140: 4.922 distance: 140 - 141: 20.104 distance: 142 - 143: 19.574 distance: 143 - 144: 13.506 distance: 143 - 146: 13.739 distance: 144 - 145: 39.092 distance: 144 - 148: 12.717 distance: 146 - 147: 14.488 distance: 148 - 149: 14.510 distance: 149 - 150: 18.912 distance: 150 - 151: 4.764 distance: 150 - 156: 14.151 distance: 152 - 153: 8.117 distance: 153 - 154: 10.180 distance: 153 - 155: 18.571 distance: 156 - 157: 5.793 distance: 157 - 158: 19.912 distance: 157 - 160: 13.397 distance: 158 - 159: 30.559 distance: 158 - 164: 22.921 distance: 160 - 161: 7.413 distance: 161 - 162: 13.892 distance: 161 - 163: 23.864