Starting phenix.real_space_refine on Fri Aug 2 14:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql3_14062/08_2024/7ql3_14062.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql3_14062/08_2024/7ql3_14062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql3_14062/08_2024/7ql3_14062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql3_14062/08_2024/7ql3_14062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql3_14062/08_2024/7ql3_14062.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql3_14062/08_2024/7ql3_14062.cif" } resolution = 3.32 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= 0.003 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 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 2.38, per 1000 atoms: 0.73 Number of scatterers: 3246 At special positions: 0 Unit cell: (95.79, 111.6, 35.34, 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 6 16.00 O 606 8.00 N 588 7.00 C 2046 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: 0.91 Conformation dependent library (CDL) restraints added in 683.9 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.734A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.758A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 3.525A pdb=" N LEU A 325 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.623A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.521A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.682A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 361 removed outlier: 6.581A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 371 Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 377 removed outlier: 6.599A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.609A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.707A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 3.582A pdb=" N LEU D 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.694A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 339 removed outlier: 6.528A pdb=" N GLN D 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL E 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.591A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 359 through 361 removed outlier: 6.580A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 368 through 371 removed outlier: 6.623A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.658A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 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: 0.70 Time building geometry restraints manager: 1.04 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: 879 1.33 - 1.45: 446 1.45 - 1.57: 1969 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3300 Sorted by residual: bond pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 1.532 1.550 -0.018 6.50e-03 2.37e+04 7.90e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.68e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.21e+00 ... (remaining 3295 not shown) Histogram of bond angle deviations from ideal: 97.08 - 103.42: 32 103.42 - 109.77: 612 109.77 - 116.12: 1582 116.12 - 122.47: 1666 122.47 - 128.82: 524 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N GLY A 323 " pdb=" CA GLY A 323 " pdb=" C GLY A 323 " ideal model delta sigma weight residual 111.14 125.39 -14.25 1.80e+00 3.09e-01 6.27e+01 angle pdb=" N SER D 356 " pdb=" CA SER D 356 " pdb=" C SER D 356 " ideal model delta sigma weight residual 111.03 117.92 -6.89 1.11e+00 8.12e-01 3.85e+01 angle pdb=" N SER A 356 " pdb=" CA SER A 356 " pdb=" C SER A 356 " ideal model delta sigma weight residual 111.03 117.88 -6.85 1.11e+00 8.12e-01 3.81e+01 angle pdb=" N SER A 324 " pdb=" CA SER A 324 " pdb=" C SER A 324 " ideal model delta sigma weight residual 108.02 97.08 10.94 1.78e+00 3.16e-01 3.78e+01 angle pdb=" N GLY D 323 " pdb=" CA GLY D 323 " pdb=" C GLY D 323 " ideal model delta sigma weight residual 110.56 120.42 -9.86 1.66e+00 3.63e-01 3.53e+01 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1791 14.12 - 28.25: 167 28.25 - 42.37: 34 42.37 - 56.50: 6 56.50 - 70.62: 6 Dihedral angle restraints: 2004 sinusoidal: 834 harmonic: 1170 Sorted by residual: dihedral pdb=" CA GLY A 323 " pdb=" C GLY A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual 180.00 149.74 30.26 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA CYS A 322 " pdb=" C CYS A 322 " pdb=" N GLY A 323 " pdb=" CA GLY A 323 " ideal model delta harmonic sigma weight residual -180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA CYS C 322 " pdb=" C CYS C 322 " pdb=" N GLY C 323 " pdb=" CA GLY C 323 " ideal model delta harmonic sigma weight residual 180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 275 0.080 - 0.160: 166 0.160 - 0.240: 36 0.240 - 0.320: 11 0.320 - 0.400: 10 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN D 351 " pdb=" N GLN D 351 " pdb=" C GLN D 351 " pdb=" CB GLN D 351 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 495 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.129 2.00e-02 2.50e+03 6.75e-02 9.11e+01 pdb=" CG TYR C 310 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.122 2.00e-02 2.50e+03 6.55e-02 8.59e+01 pdb=" CG TYR F 310 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.105 2.00e-02 2.50e+03 5.57e-02 6.20e+01 pdb=" CG TYR D 310 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.080 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1389 2.97 - 3.45: 2648 3.45 - 3.94: 4714 3.94 - 4.42: 4640 4.42 - 4.90: 9852 Nonbonded interactions: 23243 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.489 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.526 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.530 3.040 ... (remaining 23238 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 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: 0.700 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.170 Find NCS groups from input model: 0.110 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.011 0.035 3300 Z= 0.765 Angle : 2.010 14.251 4416 Z= 1.337 Chirality : 0.111 0.400 498 Planarity : 0.011 0.067 558 Dihedral : 12.269 70.619 1260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 2.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.47 (0.31), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 362 PHE 0.037 0.011 PHE B 346 TYR 0.129 0.041 TYR C 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.390 Fit side-chains REVERT: B 352 SER cc_start: 0.9293 (t) cc_final: 0.8913 (m) REVERT: E 352 SER cc_start: 0.9144 (t) cc_final: 0.8810 (m) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2430 time to fit residues: 20.9492 Evaluate side-chains 50 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 330 HIS B 374 HIS C 374 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 330 HIS E 374 HIS F 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3300 Z= 0.243 Angle : 0.851 8.456 4416 Z= 0.419 Chirality : 0.054 0.175 498 Planarity : 0.004 0.036 558 Dihedral : 6.925 20.548 432 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.08 % Allowed : 9.14 % Favored : 89.78 % 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: -2.76 (0.34), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 330 PHE 0.010 0.002 PHE F 346 TYR 0.017 0.004 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.386 Fit side-chains REVERT: B 352 SER cc_start: 0.9289 (t) cc_final: 0.8870 (m) REVERT: D 343 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8613 (mtmm) REVERT: D 348 ASP cc_start: 0.8828 (t0) cc_final: 0.8625 (t0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.2449 time to fit residues: 14.8290 Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 0.0010 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS D 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3300 Z= 0.386 Angle : 0.805 6.814 4416 Z= 0.413 Chirality : 0.055 0.160 498 Planarity : 0.006 0.052 558 Dihedral : 6.643 19.465 432 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.69 % Allowed : 10.22 % Favored : 87.10 % 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: -2.66 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS E 362 PHE 0.015 0.003 PHE F 346 TYR 0.025 0.006 TYR C 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.421 Fit side-chains REVERT: B 352 SER cc_start: 0.9299 (t) cc_final: 0.9006 (m) REVERT: C 352 SER cc_start: 0.9217 (t) cc_final: 0.8893 (m) REVERT: D 343 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8589 (mtmt) REVERT: E 343 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8422 (mttp) REVERT: F 352 SER cc_start: 0.9204 (t) cc_final: 0.8882 (m) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 0.2460 time to fit residues: 12.3091 Evaluate side-chains 36 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3300 Z= 0.366 Angle : 0.762 7.984 4416 Z= 0.391 Chirality : 0.053 0.145 498 Planarity : 0.007 0.053 558 Dihedral : 6.405 18.034 432 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.69 % Allowed : 12.10 % Favored : 85.22 % 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: -2.71 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS E 362 PHE 0.013 0.003 PHE F 346 TYR 0.023 0.005 TYR C 310 ARG 0.000 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.406 Fit side-chains REVERT: B 352 SER cc_start: 0.9251 (t) cc_final: 0.9028 (m) REVERT: C 352 SER cc_start: 0.9174 (t) cc_final: 0.8930 (m) REVERT: D 343 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8632 (mtmt) REVERT: F 352 SER cc_start: 0.9189 (t) cc_final: 0.8941 (m) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.2136 time to fit residues: 11.3959 Evaluate side-chains 39 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3300 Z= 0.272 Angle : 0.693 6.961 4416 Z= 0.351 Chirality : 0.050 0.137 498 Planarity : 0.006 0.053 558 Dihedral : 5.870 16.881 432 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.49 % Allowed : 12.37 % Favored : 84.14 % 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: -2.67 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.008 0.002 PHE F 346 TYR 0.016 0.004 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.323 Fit side-chains REVERT: B 352 SER cc_start: 0.9181 (t) cc_final: 0.8962 (m) REVERT: C 352 SER cc_start: 0.9126 (t) cc_final: 0.8921 (m) REVERT: D 343 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8627 (mtmt) REVERT: D 352 SER cc_start: 0.9212 (t) cc_final: 0.8952 (m) REVERT: F 352 SER cc_start: 0.9133 (t) cc_final: 0.8922 (m) outliers start: 13 outliers final: 6 residues processed: 50 average time/residue: 0.1463 time to fit residues: 9.1419 Evaluate side-chains 48 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0060 chunk 40 optimal weight: 0.0020 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 overall best weight: 5.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS C 329 HIS D 327 ASN F 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3300 Z= 0.347 Angle : 0.730 8.704 4416 Z= 0.373 Chirality : 0.052 0.142 498 Planarity : 0.007 0.053 558 Dihedral : 5.921 16.465 432 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.23 % Allowed : 15.05 % Favored : 81.72 % 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: -2.63 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 362 PHE 0.011 0.002 PHE F 346 TYR 0.020 0.005 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.389 Fit side-chains REVERT: B 352 SER cc_start: 0.9194 (t) cc_final: 0.8981 (m) REVERT: D 343 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8485 (mttp) REVERT: D 352 SER cc_start: 0.9222 (t) cc_final: 0.8984 (m) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.1727 time to fit residues: 11.1013 Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain E residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 50.0841 > 50: distance: 21 - 130: 13.446 distance: 24 - 145: 7.091 distance: 113 - 115: 8.655 distance: 115 - 116: 7.058 distance: 116 - 117: 7.812 distance: 117 - 119: 3.725 distance: 120 - 123: 3.476 distance: 124 - 125: 6.071 distance: 124 - 126: 3.894 distance: 127 - 128: 4.461 distance: 128 - 129: 3.504 distance: 128 - 131: 4.413 distance: 129 - 130: 5.935 distance: 129 - 136: 4.197 distance: 131 - 132: 5.531 distance: 132 - 133: 10.848 distance: 133 - 134: 9.369 distance: 134 - 135: 3.836 distance: 136 - 137: 6.208 distance: 137 - 138: 6.421 distance: 137 - 140: 4.696 distance: 138 - 139: 4.684 distance: 138 - 145: 7.310 distance: 140 - 141: 12.167 distance: 141 - 142: 11.237 distance: 142 - 143: 10.555 distance: 143 - 144: 5.983 distance: 145 - 146: 4.061 distance: 146 - 147: 7.067 distance: 146 - 149: 8.584 distance: 147 - 148: 7.700 distance: 147 - 153: 10.074 distance: 149 - 150: 8.633 distance: 149 - 151: 6.232 distance: 150 - 152: 8.458 distance: 153 - 154: 11.333 distance: 154 - 155: 4.905 distance: 154 - 157: 6.000 distance: 155 - 162: 8.120 distance: 157 - 158: 12.680 distance: 158 - 159: 8.516 distance: 159 - 160: 5.554 distance: 163 - 164: 5.773 distance: 163 - 166: 4.462 distance: 164 - 165: 4.096 distance: 164 - 169: 3.813 distance: 166 - 167: 10.136 distance: 166 - 168: 17.976 distance: 169 - 170: 10.426 distance: 170 - 171: 7.199 distance: 171 - 172: 5.521 distance: 171 - 179: 11.703 distance: 173 - 174: 7.089 distance: 174 - 175: 3.434 distance: 174 - 176: 3.430 distance: 175 - 177: 3.384 distance: 176 - 178: 10.794 distance: 177 - 178: 6.503 distance: 179 - 180: 6.719 distance: 180 - 181: 4.594 distance: 180 - 183: 10.485 distance: 181 - 182: 29.631 distance: 181 - 188: 22.010 distance: 183 - 184: 6.168 distance: 184 - 185: 5.439 distance: 185 - 186: 11.071 distance: 186 - 187: 8.278 distance: 188 - 189: 23.667 distance: 189 - 190: 5.791 distance: 189 - 192: 7.990 distance: 190 - 191: 13.859 distance: 190 - 196: 12.636 distance: 192 - 193: 5.826 distance: 193 - 194: 6.368 distance: 193 - 195: 4.600