Starting phenix.real_space_refine on Thu Jan 18 01:41:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhq_29099/01_2024/8fhq_29099_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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: 7 Type Number sf(0) Gaussians S 48 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 4836 2.51 5 N 1144 2.21 5 O 1268 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ASP 332": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3627 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3627 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.48, per 1000 atoms: 0.61 Number of scatterers: 7306 At special positions: 0 Unit cell: (92.02, 105.78, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 48 16.00 Na 2 11.00 F 6 9.00 O 1268 8.00 N 1144 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.509A pdb=" N ALA A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 4.042A pdb=" N VAL A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 4.326A pdb=" N LEU A 206 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 210 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 249 removed outlier: 3.543A pdb=" N GLY A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 Processing helix chain 'A' and resid 280 through 305 removed outlier: 3.900A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.601A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 367 through 393 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.701A pdb=" N SER A 422 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 454 through 483 removed outlier: 4.393A pdb=" N LEU A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 479 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.753A pdb=" N LEU A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 552 removed outlier: 3.520A pdb=" N PHE A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.605A pdb=" N VAL A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.509A pdb=" N ALA B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 195 removed outlier: 4.041A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 4.326A pdb=" N LEU B 206 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 208 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 210 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 249 removed outlier: 3.543A pdb=" N GLY B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 276 Processing helix chain 'B' and resid 280 through 305 removed outlier: 3.900A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.601A pdb=" N VAL B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 367 through 393 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 419 through 423 removed outlier: 3.701A pdb=" N SER B 422 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 454 through 483 removed outlier: 4.393A pdb=" N LEU B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 495 No H-bonds generated for 'chain 'B' and resid 493 through 495' Processing helix chain 'B' and resid 506 through 522 removed outlier: 3.753A pdb=" N LEU B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 552 removed outlier: 3.521A pdb=" N PHE B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.605A pdb=" N VAL B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 412 hydrogen bonds defined for protein. 1074 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: 1.82 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1102 1.31 - 1.44: 2154 1.44 - 1.56: 4170 1.56 - 1.69: 6 1.69 - 1.81: 72 Bond restraints: 7504 Sorted by residual: bond pdb=" C ASN B 149 " pdb=" O ASN B 149 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.29e-02 6.01e+03 1.30e+01 bond pdb=" C ASN A 149 " pdb=" O ASN A 149 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.29e-02 6.01e+03 1.25e+01 bond pdb=" C ASN B 149 " pdb=" N ILE B 150 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.26e-02 6.30e+03 6.76e+00 bond pdb=" C16 XZF B1101 " pdb=" C17 XZF B1101 " ideal model delta sigma weight residual 1.368 1.317 0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C16 XZF A1101 " pdb=" C17 XZF A1101 " ideal model delta sigma weight residual 1.368 1.317 0.051 2.00e-02 2.50e+03 6.53e+00 ... (remaining 7499 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.19: 164 106.19 - 113.17: 4054 113.17 - 120.14: 2873 120.14 - 127.12: 3078 127.12 - 134.09: 87 Bond angle restraints: 10256 Sorted by residual: angle pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " ideal model delta sigma weight residual 112.60 118.90 -6.30 1.70e+00 3.46e-01 1.37e+01 angle pdb=" CB GLU B 310 " pdb=" CG GLU B 310 " pdb=" CD GLU B 310 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.70e+00 3.46e-01 1.35e+01 angle pdb=" C VAL A 254 " pdb=" N ASP A 255 " pdb=" CA ASP A 255 " ideal model delta sigma weight residual 122.15 109.58 12.57 3.47e+00 8.31e-02 1.31e+01 angle pdb=" C VAL B 254 " pdb=" N ASP B 255 " pdb=" CA ASP B 255 " ideal model delta sigma weight residual 122.15 109.60 12.55 3.47e+00 8.31e-02 1.31e+01 angle pdb=" CA LEU A 148 " pdb=" C LEU A 148 " pdb=" N ASN A 149 " ideal model delta sigma weight residual 117.72 122.24 -4.52 1.31e+00 5.83e-01 1.19e+01 ... (remaining 10251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3893 17.83 - 35.67: 308 35.67 - 53.50: 47 53.50 - 71.33: 16 71.33 - 89.16: 6 Dihedral angle restraints: 4270 sinusoidal: 1560 harmonic: 2710 Sorted by residual: dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 139.01 -46.01 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 4267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 641 0.036 - 0.071: 381 0.071 - 0.107: 121 0.107 - 0.142: 44 0.142 - 0.178: 5 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA ASN B 149 " pdb=" N ASN B 149 " pdb=" C ASN B 149 " pdb=" CB ASN B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CG LEU A 583 " pdb=" CB LEU A 583 " pdb=" CD1 LEU A 583 " pdb=" CD2 LEU A 583 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1189 not shown) Planarity restraints: 1246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 255 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO A 256 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 255 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO B 256 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 318 " -0.019 2.00e-02 2.50e+03 1.73e-02 5.21e+00 pdb=" CG PHE A 318 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 318 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 318 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 318 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 318 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 318 " -0.006 2.00e-02 2.50e+03 ... (remaining 1243 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2259 2.82 - 3.34: 6999 3.34 - 3.86: 11743 3.86 - 4.38: 14200 4.38 - 4.90: 24175 Nonbonded interactions: 59376 Sorted by model distance: nonbonded pdb=" O LEU A 148 " pdb="NA NA A1102 " model vdw 2.303 2.470 nonbonded pdb=" O LEU B 148 " pdb="NA NA B1102 " model vdw 2.304 2.470 nonbonded pdb=" O ALA B 464 " pdb="NA NA B1102 " model vdw 2.324 2.470 nonbonded pdb=" O ALA A 464 " pdb="NA NA A1102 " model vdw 2.325 2.470 nonbonded pdb=" O TRP A 151 " pdb="NA NA A1102 " model vdw 2.376 2.470 ... (remaining 59371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.090 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: 0.010 Extract box with map and model: 7.120 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.490 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.056 7504 Z= 0.533 Angle : 0.821 12.574 10256 Z= 0.440 Chirality : 0.050 0.178 1192 Planarity : 0.006 0.060 1246 Dihedral : 13.692 89.162 2534 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.65 % Allowed : 0.78 % Favored : 98.56 % 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: -1.14 (0.25), residues: 946 helix: -0.12 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -2.05 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 425 HIS 0.003 0.001 HIS B 434 PHE 0.039 0.002 PHE A 318 TYR 0.014 0.002 TYR B 438 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.709 Fit side-chains REVERT: B 310 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: B 332 ASP cc_start: 0.8071 (t70) cc_final: 0.7743 (t0) outliers start: 5 outliers final: 0 residues processed: 88 average time/residue: 1.0443 time to fit residues: 98.1827 Evaluate side-chains 74 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7504 Z= 0.192 Angle : 0.518 5.415 10256 Z= 0.275 Chirality : 0.039 0.155 1192 Planarity : 0.005 0.047 1246 Dihedral : 6.436 82.719 1029 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.17 % Allowed : 5.87 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 946 helix: 0.76 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.78 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 425 HIS 0.005 0.002 HIS A 234 PHE 0.012 0.001 PHE A 340 TYR 0.007 0.001 TYR B 438 ARG 0.005 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.808 Fit side-chains REVERT: A 366 ASP cc_start: 0.8515 (p0) cc_final: 0.8276 (p0) REVERT: B 310 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: B 366 ASP cc_start: 0.8456 (p0) cc_final: 0.8228 (p0) REVERT: B 377 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7759 (mmt) outliers start: 9 outliers final: 2 residues processed: 81 average time/residue: 0.9420 time to fit residues: 82.8732 Evaluate side-chains 74 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7504 Z= 0.346 Angle : 0.599 5.975 10256 Z= 0.309 Chirality : 0.043 0.172 1192 Planarity : 0.005 0.046 1246 Dihedral : 6.490 80.162 1029 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.70 % Allowed : 9.66 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 946 helix: 0.56 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -1.71 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 425 HIS 0.005 0.002 HIS B 234 PHE 0.023 0.002 PHE A 318 TYR 0.010 0.001 TYR B 438 ARG 0.004 0.001 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.728 Fit side-chains REVERT: A 366 ASP cc_start: 0.8554 (p0) cc_final: 0.8274 (p0) REVERT: B 366 ASP cc_start: 0.8548 (p0) cc_final: 0.8246 (p0) REVERT: B 377 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7798 (mmt) outliers start: 13 outliers final: 4 residues processed: 79 average time/residue: 0.9730 time to fit residues: 82.7239 Evaluate side-chains 76 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.0170 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.8159 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7504 Z= 0.156 Angle : 0.465 4.963 10256 Z= 0.244 Chirality : 0.038 0.159 1192 Planarity : 0.004 0.040 1246 Dihedral : 5.462 58.918 1026 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.31 % Allowed : 10.70 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 946 helix: 1.05 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.55 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 425 HIS 0.003 0.001 HIS A 234 PHE 0.009 0.001 PHE B 340 TYR 0.006 0.001 TYR B 438 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.809 Fit side-chains REVERT: A 366 ASP cc_start: 0.8431 (p0) cc_final: 0.8139 (p0) REVERT: A 405 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6848 (tt) REVERT: B 366 ASP cc_start: 0.8374 (p0) cc_final: 0.8014 (p0) REVERT: B 377 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (mmm) REVERT: B 430 CYS cc_start: 0.3663 (OUTLIER) cc_final: 0.3358 (t) outliers start: 10 outliers final: 1 residues processed: 80 average time/residue: 0.9494 time to fit residues: 81.8305 Evaluate side-chains 74 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 430 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 0.0070 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- 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: 0.8171 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7504 Z= 0.182 Angle : 0.481 5.830 10256 Z= 0.249 Chirality : 0.039 0.161 1192 Planarity : 0.004 0.037 1246 Dihedral : 5.328 57.891 1026 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.31 % Allowed : 12.01 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 946 helix: 1.13 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.50 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 425 HIS 0.002 0.001 HIS A 234 PHE 0.011 0.001 PHE A 340 TYR 0.008 0.001 TYR A 438 ARG 0.003 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.716 Fit side-chains REVERT: A 366 ASP cc_start: 0.8433 (p0) cc_final: 0.8032 (p0) REVERT: A 405 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.6923 (tt) REVERT: B 366 ASP cc_start: 0.8350 (p0) cc_final: 0.8004 (p0) REVERT: B 377 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7784 (mmt) REVERT: B 430 CYS cc_start: 0.3556 (OUTLIER) cc_final: 0.3176 (t) outliers start: 10 outliers final: 2 residues processed: 78 average time/residue: 0.9257 time to fit residues: 77.8073 Evaluate side-chains 74 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 430 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 52.533 > 50: distance: 54 - 79: 15.306 distance: 56 - 57: 4.458 distance: 56 - 62: 8.681 distance: 57 - 58: 4.380 distance: 57 - 60: 4.107 distance: 58 - 59: 22.626 distance: 58 - 63: 20.430 distance: 59 - 85: 15.265 distance: 60 - 61: 12.683 distance: 63 - 64: 18.426 distance: 64 - 65: 19.062 distance: 64 - 67: 20.827 distance: 65 - 66: 18.787 distance: 65 - 71: 19.321 distance: 66 - 93: 17.823 distance: 67 - 68: 6.177 distance: 67 - 69: 11.886 distance: 68 - 70: 9.158 distance: 71 - 72: 25.876 distance: 72 - 73: 13.278 distance: 72 - 75: 12.510 distance: 73 - 74: 13.547 distance: 73 - 79: 5.613 distance: 75 - 76: 10.321 distance: 75 - 77: 15.643 distance: 76 - 78: 17.929 distance: 80 - 81: 4.129 distance: 80 - 83: 3.734 distance: 81 - 82: 7.538 distance: 83 - 84: 10.855 distance: 85 - 86: 8.179 distance: 86 - 87: 5.995 distance: 86 - 89: 4.087 distance: 87 - 88: 5.213 distance: 87 - 93: 6.162 distance: 88 - 123: 12.494 distance: 89 - 90: 8.541 distance: 90 - 91: 8.675 distance: 90 - 92: 4.466 distance: 93 - 94: 3.144 distance: 94 - 95: 4.336 distance: 94 - 97: 8.175 distance: 95 - 96: 4.187 distance: 95 - 104: 9.530 distance: 97 - 98: 4.528 distance: 98 - 99: 6.562 distance: 98 - 100: 3.094 distance: 99 - 101: 5.809 distance: 100 - 102: 4.082 distance: 102 - 103: 6.441 distance: 104 - 105: 6.517 distance: 105 - 106: 5.469 distance: 105 - 108: 5.000 distance: 106 - 107: 3.796 distance: 106 - 115: 7.722 distance: 107 - 135: 9.510 distance: 108 - 109: 6.512 distance: 109 - 110: 8.882 distance: 109 - 111: 5.970 distance: 110 - 112: 6.485 distance: 112 - 114: 7.484 distance: 113 - 114: 5.806 distance: 115 - 116: 14.261 distance: 116 - 117: 5.898 distance: 116 - 119: 15.505 distance: 117 - 118: 9.506 distance: 117 - 123: 6.076 distance: 118 - 144: 8.901 distance: 119 - 120: 5.024 distance: 120 - 121: 7.643 distance: 120 - 122: 13.268 distance: 123 - 124: 6.098 distance: 124 - 125: 16.887 distance: 124 - 127: 6.927 distance: 125 - 126: 9.729 distance: 125 - 129: 11.703 distance: 126 - 148: 10.805 distance: 127 - 128: 3.868 distance: 129 - 130: 9.687 distance: 130 - 133: 8.498 distance: 133 - 134: 3.959 distance: 138 - 162: 3.010