Starting phenix.real_space_refine (version: dev) on Sun Mar 12 03:21:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2023/7fil_31602.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2023/7fil_31602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2023/7fil_31602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2023/7fil_31602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2023/7fil_31602.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2023/7fil_31602.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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 Process input model Symmetric amino acids flipped Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A ASP 665": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ASP 696": "OD1" <-> "OD2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 722": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 3993 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3993 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 481} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.84, per 1000 atoms: 0.71 Number of scatterers: 3993 At special positions: 0 Unit cell: (76.285, 77.672, 102.638, 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 22 16.00 O 747 8.00 N 673 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 658.1 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 67.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 222 through 243 removed outlier: 4.095A pdb=" N LYS A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.565A pdb=" N LYS A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.452A pdb=" N VAL A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 3.654A pdb=" N ALA A 322 " --> pdb=" O CYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 362 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.800A pdb=" N SER A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 4.342A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.880A pdb=" N SER A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.683A pdb=" N TRP A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.536A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.940A pdb=" N LEU A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 4.195A pdb=" N GLU A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.555A pdb=" N LEU A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.511A pdb=" N ILE A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 690 removed outlier: 3.508A pdb=" N TYR A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.824A pdb=" N GLU A 701 " --> pdb=" O CYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 3.683A pdb=" N ALA A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Proline residue: A 728 - end of helix 235 hydrogen bonds defined for protein. 705 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: 1.02 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1056 1.33 - 1.45: 701 1.45 - 1.57: 2286 1.57 - 1.69: 1 1.69 - 1.82: 31 Bond restraints: 4075 Sorted by residual: bond pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 1.469 1.692 -0.223 1.28e-02 6.10e+03 3.05e+02 bond pdb=" C LYS A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.333 1.499 -0.167 1.17e-02 7.31e+03 2.03e+02 bond pdb=" C VAL A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.332 1.509 -0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C GLU A 313 " pdb=" N PRO A 314 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.34e-02 1.83e+03 2.48e+01 bond pdb=" N LYS A 365 " pdb=" CA LYS A 365 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.02e+00 ... (remaining 4070 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.30: 71 105.30 - 113.22: 2301 113.22 - 121.14: 2168 121.14 - 129.06: 943 129.06 - 136.98: 38 Bond angle restraints: 5521 Sorted by residual: angle pdb=" C LYS A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta sigma weight residual 119.90 136.48 -16.58 1.05e+00 9.07e-01 2.49e+02 angle pdb=" C VAL A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 119.76 134.51 -14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C GLU A 313 " pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 119.84 136.98 -17.14 1.25e+00 6.40e-01 1.88e+02 angle pdb=" N PRO A 314 " pdb=" CA PRO A 314 " pdb=" C PRO A 314 " ideal model delta sigma weight residual 112.47 97.38 15.09 2.06e+00 2.36e-01 5.37e+01 angle pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" CD PRO A 314 " ideal model delta sigma weight residual 112.00 101.88 10.12 1.40e+00 5.10e-01 5.23e+01 ... (remaining 5516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2098 17.76 - 35.52: 261 35.52 - 53.28: 80 53.28 - 71.04: 23 71.04 - 88.80: 7 Dihedral angle restraints: 2469 sinusoidal: 982 harmonic: 1487 Sorted by residual: dihedral pdb=" CA GLN A 564 " pdb=" C GLN A 564 " pdb=" N GLU A 565 " pdb=" CA GLU A 565 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" C TYR A 597 " pdb=" N TYR A 597 " pdb=" CA TYR A 597 " pdb=" CB TYR A 597 " ideal model delta harmonic sigma weight residual -122.60 -133.07 10.47 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA PRO A 462 " pdb=" C PRO A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta harmonic sigma weight residual 180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 607 0.128 - 0.257: 15 0.257 - 0.385: 3 0.385 - 0.513: 0 0.513 - 0.641: 1 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" C PRO A 314 " pdb=" CB PRO A 314 " both_signs ideal model delta sigma weight residual False 2.72 3.36 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TYR A 597 " pdb=" N TYR A 597 " pdb=" C TYR A 597 " pdb=" CB TYR A 597 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA LYS A 327 " pdb=" N LYS A 327 " pdb=" C LYS A 327 " pdb=" CB LYS A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 623 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 322 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C ALA A 322 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 323 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 360 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 360 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 360 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 314 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PRO A 314 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 315 " -0.012 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 597 2.75 - 3.29: 4096 3.29 - 3.83: 6537 3.83 - 4.36: 7249 4.36 - 4.90: 12045 Nonbonded interactions: 30524 Sorted by model distance: nonbonded pdb=" O PHE A 632 " pdb=" N ASN A 634 " model vdw 2.213 2.520 nonbonded pdb=" O SER A 478 " pdb=" OG SER A 478 " model vdw 2.218 2.440 nonbonded pdb=" OG SER A 352 " pdb=" OD1 ASP A 423 " model vdw 2.224 2.440 nonbonded pdb=" ND2 ASN A 474 " pdb=" OG1 THR A 559 " model vdw 2.237 2.520 nonbonded pdb=" OE1 GLN A 324 " pdb=" NH1 ARG A 412 " model vdw 2.253 2.520 ... (remaining 30519 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2551 2.51 5 N 673 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 2.080 Check model and map are aligned: 0.060 Process input model: 15.060 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.008 0.223 4075 Z= 0.513 Angle : 1.046 17.138 5521 Z= 0.706 Chirality : 0.062 0.641 626 Planarity : 0.005 0.040 705 Dihedral : 18.460 88.802 1497 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.66 % Favored : 91.13 % Rotamer Outliers : 8.76 % Cbeta Deviations : 0.41 % 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: -1.82 (0.36), residues: 496 helix: -0.21 (0.27), residues: 318 sheet: None (None), residues: 0 loop : -3.06 (0.43), residues: 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 0.521 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 106 average time/residue: 1.0036 time to fit residues: 110.5161 Evaluate side-chains 72 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2209 time to fit residues: 0.9141 ------------------------------------------------------------------------------- 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-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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: 50.8981 > 50: distance: 37 - 45: 3.195 distance: 78 - 84: 5.510 distance: 84 - 85: 6.193 distance: 84 - 90: 7.432 distance: 85 - 86: 4.735 distance: 85 - 88: 7.548 distance: 86 - 87: 11.530 distance: 86 - 91: 6.143 distance: 88 - 89: 11.270 distance: 89 - 90: 13.540 distance: 91 - 92: 3.519 distance: 92 - 93: 8.940 distance: 92 - 95: 6.805 distance: 93 - 94: 7.790 distance: 93 - 99: 4.547 distance: 95 - 96: 4.162 distance: 95 - 97: 7.823 distance: 96 - 98: 10.202 distance: 99 - 100: 6.848 distance: 100 - 101: 8.655 distance: 100 - 103: 4.779 distance: 101 - 102: 7.104 distance: 101 - 105: 12.924 distance: 103 - 104: 11.427 distance: 105 - 106: 5.946 distance: 106 - 107: 7.451 distance: 106 - 109: 4.739 distance: 110 - 111: 13.242 distance: 111 - 112: 6.219 distance: 112 - 113: 9.390 distance: 114 - 115: 7.166 distance: 115 - 116: 12.993 distance: 115 - 118: 12.246 distance: 116 - 117: 14.271 distance: 116 - 123: 23.182 distance: 118 - 119: 14.521 distance: 119 - 120: 5.044 distance: 120 - 121: 18.081 distance: 120 - 122: 13.044 distance: 123 - 124: 16.722 distance: 124 - 125: 11.956 distance: 124 - 127: 17.749 distance: 125 - 126: 12.918 distance: 125 - 131: 7.555 distance: 127 - 128: 19.479 distance: 128 - 129: 12.343 distance: 128 - 130: 27.664 distance: 131 - 132: 4.732 distance: 132 - 133: 11.310 distance: 132 - 135: 7.691 distance: 133 - 134: 4.718 distance: 133 - 142: 8.488 distance: 135 - 136: 3.743 distance: 136 - 137: 3.849 distance: 136 - 138: 5.728 distance: 137 - 139: 4.469 distance: 138 - 140: 5.932 distance: 139 - 141: 3.255 distance: 140 - 141: 6.120 distance: 142 - 143: 4.688 distance: 143 - 146: 11.024 distance: 144 - 145: 6.212 distance: 145 - 177: 4.675 distance: 146 - 147: 11.028 distance: 146 - 148: 5.770 distance: 151 - 157: 4.141 distance: 152 - 188: 5.632 distance: 153 - 154: 5.383 distance: 154 - 155: 4.439 distance: 157 - 158: 4.465 distance: 158 - 159: 4.244 distance: 158 - 161: 4.122 distance: 159 - 160: 4.151 distance: 159 - 168: 3.792 distance: 160 - 194: 3.992 distance: 162 - 163: 3.749 distance: 163 - 164: 4.431 distance: 165 - 166: 5.372 distance: 165 - 167: 6.121