Starting phenix.real_space_refine on Wed Jan 17 19:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/01_2024/6y3y_10676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/01_2024/6y3y_10676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/01_2024/6y3y_10676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/01_2024/6y3y_10676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/01_2024/6y3y_10676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/01_2024/6y3y_10676.pdb" } resolution = 3.39 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= 0.006 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3778 2.51 5 N 886 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5854 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2707 Classifications: {'peptide': 332} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2707 Classifications: {'peptide': 332} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 NAG A 406 " occ=0.81 ... (12 atoms not shown) pdb=" O7 NAG A 406 " occ=0.81 residue: pdb=" C1 NAG A 407 " occ=0.44 ... (12 atoms not shown) pdb=" O7 NAG A 407 " occ=0.44 residue: pdb=" C1 NAG B 406 " occ=0.81 ... (12 atoms not shown) pdb=" O7 NAG B 406 " occ=0.81 residue: pdb=" C1 NAG B 407 " occ=0.44 ... (12 atoms not shown) pdb=" O7 NAG B 407 " occ=0.44 Time building chain proxies: 3.73, per 1000 atoms: 0.64 Number of scatterers: 5854 At special positions: 0 Unit cell: (105.455, 73.255, 88.55, 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 26 16.00 O 1164 8.00 N 886 7.00 C 3778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 154 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 154 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 341 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 405 " - " ASN A 110 " " NAG A 406 " - " ASN A 145 " " NAG A 407 " - " ASN A 193 " " NAG B 405 " - " ASN B 110 " " NAG B 406 " - " ASN B 145 " " NAG B 407 " - " ASN B 193 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 286 " " NAG E 1 " - " ASN A 314 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN B 83 " " NAG H 1 " - " ASN B 286 " " NAG I 1 " - " ASN B 314 " " NAG J 1 " - " ASN B 328 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 17.2% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.738A pdb=" N ASP A 37 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.518A pdb=" N LEU A 44 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 113 through 132 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 310 through 313 removed outlier: 3.689A pdb=" N TYR A 313 " --> pdb=" O GLY A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'B' and resid 33 through 37 removed outlier: 3.737A pdb=" N ASP B 37 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.517A pdb=" N LEU B 44 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 113 through 132 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 310 through 313 removed outlier: 3.689A pdb=" N TYR B 313 " --> pdb=" O GLY B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 8.627A pdb=" N SER A 65 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 30 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 29 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 91 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 259 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 93 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 8.426A pdb=" N LYS A 243 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 184 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 176 removed outlier: 3.733A pdb=" N VAL A 173 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197 removed outlier: 4.276A pdb=" N VAL A 206 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 208 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 208 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 206 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65 removed outlier: 8.627A pdb=" N SER B 65 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 30 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 29 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 91 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL B 259 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 93 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 removed outlier: 8.426A pdb=" N LYS B 243 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 184 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.732A pdb=" N VAL B 173 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 318 120 hydrogen bonds defined for protein. 312 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: 1.44 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1682 1.34 - 1.46: 1772 1.46 - 1.58: 2546 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 6028 Sorted by residual: bond pdb=" C PHE A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.20e+01 bond pdb=" C PHE B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.20e+01 bond pdb=" C1 NAG B 405 " pdb=" O5 NAG B 405 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG A 405 " pdb=" O5 NAG A 405 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 6023 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 244 107.29 - 113.96: 3316 113.96 - 120.63: 2379 120.63 - 127.31: 2201 127.31 - 133.98: 58 Bond angle restraints: 8198 Sorted by residual: angle pdb=" C PHE A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.84 131.88 -12.04 1.25e+00 6.40e-01 9.27e+01 angle pdb=" C PHE B 108 " pdb=" N PRO B 109 " pdb=" CA PRO B 109 " ideal model delta sigma weight residual 119.84 131.84 -12.00 1.25e+00 6.40e-01 9.22e+01 angle pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 118.56 125.78 -7.22 1.31e+00 5.83e-01 3.03e+01 angle pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 118.56 125.74 -7.18 1.31e+00 5.83e-01 3.00e+01 angle pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" O PHE B 108 " ideal model delta sigma weight residual 119.22 114.87 4.35 1.02e+00 9.61e-01 1.82e+01 ... (remaining 8193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 3606 21.52 - 43.04: 138 43.04 - 64.56: 20 64.56 - 86.07: 38 86.07 - 107.59: 24 Dihedral angle restraints: 3826 sinusoidal: 1846 harmonic: 1980 Sorted by residual: dihedral pdb=" CA ASN A 168 " pdb=" C ASN A 168 " pdb=" N TYR A 169 " pdb=" CA TYR A 169 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASN B 168 " pdb=" C ASN B 168 " pdb=" N TYR B 169 " pdb=" CA TYR B 169 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER A 147 " pdb=" C SER A 147 " pdb=" N LEU A 148 " pdb=" CA LEU A 148 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 780 0.076 - 0.152: 155 0.152 - 0.228: 17 0.228 - 0.305: 8 0.305 - 0.381: 4 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B 406 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B 406 " pdb=" O5 NAG B 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 961 not shown) Planarity restraints: 1006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 107 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C CYS A 107 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS A 107 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 108 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 107 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C CYS B 107 " 0.057 2.00e-02 2.50e+03 pdb=" O CYS B 107 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 108 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 100 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 101 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.032 5.00e-02 4.00e+02 ... (remaining 1003 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1822 2.82 - 3.34: 4959 3.34 - 3.86: 10213 3.86 - 4.38: 11600 4.38 - 4.90: 20014 Nonbonded interactions: 48608 Sorted by model distance: nonbonded pdb=" O PHE A 253 " pdb=" OH TYR B 336 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR A 336 " pdb=" O PHE B 253 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR A 283 " pdb=" O TYR A 336 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR B 283 " pdb=" O TYR B 336 " model vdw 2.305 2.440 nonbonded pdb=" OG SER B 319 " pdb=" O GLY B 322 " model vdw 2.344 2.440 ... (remaining 48603 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' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 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: 2.290 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: 6.900 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.200 Find NCS groups from input model: 0.290 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.169 6028 Z= 0.473 Angle : 1.042 12.036 8198 Z= 0.512 Chirality : 0.067 0.381 964 Planarity : 0.007 0.058 992 Dihedral : 17.443 107.593 2530 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -4.44 (0.27), residues: 660 helix: -2.69 (0.36), residues: 102 sheet: -2.19 (0.39), residues: 172 loop : -3.54 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 116 HIS 0.004 0.001 HIS B 40 PHE 0.026 0.003 PHE B 93 TYR 0.025 0.003 TYR B 128 ARG 0.004 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7501 (pp20) REVERT: A 155 LYS cc_start: 0.7031 (pmtt) cc_final: 0.5975 (tptt) REVERT: A 316 SER cc_start: 0.8801 (m) cc_final: 0.8558 (p) REVERT: B 95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7478 (pp20) REVERT: B 155 LYS cc_start: 0.7056 (pmtt) cc_final: 0.6018 (tptt) REVERT: B 316 SER cc_start: 0.8775 (m) cc_final: 0.8527 (p) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.2058 time to fit residues: 37.8651 Evaluate side-chains 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain B residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.0980 chunk 50 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6028 Z= 0.181 Angle : 0.683 9.001 8198 Z= 0.333 Chirality : 0.055 0.526 964 Planarity : 0.005 0.041 992 Dihedral : 16.129 77.072 1320 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.61 % Allowed : 8.14 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.48 (0.30), residues: 660 helix: -1.14 (0.49), residues: 102 sheet: -1.87 (0.38), residues: 176 loop : -2.98 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 116 HIS 0.003 0.001 HIS B 40 PHE 0.015 0.002 PHE A 78 TYR 0.015 0.001 TYR A 102 ARG 0.001 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7801 (pp20) cc_final: 0.7434 (pp20) REVERT: A 155 LYS cc_start: 0.6867 (pmtt) cc_final: 0.5908 (tptt) REVERT: A 197 TYR cc_start: 0.8510 (m-80) cc_final: 0.8098 (m-80) REVERT: A 316 SER cc_start: 0.8698 (m) cc_final: 0.8431 (p) REVERT: B 95 GLU cc_start: 0.7785 (pp20) cc_final: 0.7387 (pp20) REVERT: B 155 LYS cc_start: 0.6900 (pmtt) cc_final: 0.5996 (tptt) REVERT: B 316 SER cc_start: 0.8714 (m) cc_final: 0.8468 (p) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1702 time to fit residues: 23.1224 Evaluate side-chains 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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: 0.8186 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6028 Z= 0.238 Angle : 0.647 9.925 8198 Z= 0.311 Chirality : 0.051 0.424 964 Planarity : 0.005 0.036 992 Dihedral : 12.204 60.082 1320 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.61 % Allowed : 10.10 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.92 (0.31), residues: 660 helix: -0.41 (0.55), residues: 102 sheet: -1.51 (0.38), residues: 180 loop : -2.70 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.003 0.001 HIS A 299 PHE 0.014 0.002 PHE A 151 TYR 0.015 0.002 TYR B 102 ARG 0.004 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7780 (pp20) cc_final: 0.7368 (pp20) REVERT: A 316 SER cc_start: 0.8700 (m) cc_final: 0.8449 (p) REVERT: B 95 GLU cc_start: 0.7776 (pp20) cc_final: 0.7370 (pp20) REVERT: B 316 SER cc_start: 0.8693 (m) cc_final: 0.8418 (p) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.1709 time to fit residues: 22.3702 Evaluate side-chains 88 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6028 Z= 0.237 Angle : 0.622 9.387 8198 Z= 0.300 Chirality : 0.050 0.412 964 Planarity : 0.005 0.038 992 Dihedral : 9.394 54.772 1320 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.44 % Allowed : 11.40 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.68 (0.32), residues: 660 helix: -0.00 (0.57), residues: 102 sheet: -1.40 (0.39), residues: 180 loop : -2.59 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.003 0.001 HIS A 103 PHE 0.016 0.002 PHE A 139 TYR 0.018 0.002 TYR A 295 ARG 0.005 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7771 (pp20) cc_final: 0.7357 (pp20) REVERT: A 197 TYR cc_start: 0.8527 (m-80) cc_final: 0.8042 (m-80) REVERT: A 316 SER cc_start: 0.8708 (m) cc_final: 0.8439 (p) REVERT: B 95 GLU cc_start: 0.7745 (pp20) cc_final: 0.7357 (pp20) REVERT: B 316 SER cc_start: 0.8705 (m) cc_final: 0.8421 (p) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 0.1692 time to fit residues: 20.2920 Evaluate side-chains 84 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 51.0342 > 50: distance: 17 - 217: 13.174 distance: 30 - 199: 11.607 distance: 33 - 196: 10.560 distance: 158 - 162: 3.348 distance: 162 - 163: 9.566 distance: 163 - 164: 6.220 distance: 163 - 166: 12.689 distance: 164 - 165: 25.573 distance: 164 - 170: 25.519 distance: 166 - 167: 9.260 distance: 167 - 168: 9.831 distance: 167 - 169: 15.040 distance: 170 - 171: 11.987 distance: 171 - 172: 7.068 distance: 171 - 174: 9.124 distance: 172 - 173: 6.670 distance: 172 - 179: 8.199 distance: 174 - 175: 10.048 distance: 175 - 176: 11.707 distance: 176 - 177: 21.943 distance: 177 - 178: 19.821 distance: 179 - 180: 12.289 distance: 179 - 185: 20.903 distance: 180 - 181: 10.048 distance: 180 - 183: 7.901 distance: 181 - 182: 9.695 distance: 181 - 186: 7.694 distance: 183 - 184: 31.179 distance: 184 - 185: 7.938 distance: 186 - 187: 5.933 distance: 187 - 188: 11.982 distance: 188 - 189: 4.551 distance: 188 - 190: 11.118 distance: 190 - 191: 5.571 distance: 191 - 192: 5.897 distance: 191 - 194: 4.406 distance: 192 - 193: 4.537 distance: 192 - 196: 3.864 distance: 194 - 195: 5.032 distance: 197 - 198: 8.915 distance: 197 - 200: 3.813 distance: 198 - 199: 9.249 distance: 198 - 208: 7.789 distance: 200 - 201: 5.242 distance: 201 - 202: 5.796 distance: 201 - 203: 14.490 distance: 202 - 204: 10.136 distance: 203 - 205: 11.361 distance: 204 - 206: 12.194 distance: 205 - 206: 3.347 distance: 206 - 207: 6.356 distance: 208 - 209: 11.101 distance: 209 - 212: 7.651 distance: 210 - 211: 18.827 distance: 210 - 217: 16.662 distance: 212 - 213: 6.982 distance: 213 - 214: 13.060 distance: 214 - 215: 21.134 distance: 215 - 216: 4.847 distance: 217 - 218: 14.276 distance: 218 - 219: 8.390 distance: 218 - 221: 11.637 distance: 219 - 220: 5.912 distance: 219 - 224: 8.408 distance: 221 - 222: 4.460 distance: 221 - 223: 4.720 distance: 224 - 225: 11.033 distance: 225 - 226: 4.298 distance: 225 - 228: 4.970 distance: 226 - 227: 14.836 distance: 226 - 230: 5.142 distance: 228 - 229: 9.263 distance: 230 - 231: 19.520 distance: 231 - 232: 7.332 distance: 231 - 234: 19.128 distance: 232 - 233: 14.045 distance: 232 - 237: 9.389 distance: 234 - 235: 10.457 distance: 234 - 236: 15.416