Starting phenix.real_space_refine on Tue Apr 9 08:42:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzk_14389/04_2024/7yzk_14389_trim_updated.pdb" } resolution = 3.57 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 724 atoms to isotropic. 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 Mn 4 7.51 5 P 6 5.49 5 S 26 5.16 5 C 4850 2.51 5 N 1312 2.21 5 O 1424 1.98 5 H 7522 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15144 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5776 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 5775 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 5775 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 bond proxies already assigned to first conformer: 5836 Chain: "B" Number of atoms: 5776 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 5775 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 5775 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 bond proxies already assigned to first conformer: 5836 Chain: "C" Number of atoms: 1752 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} bond proxies already assigned to first conformer: 1686 Chain: "D" Number of atoms: 1752 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} bond proxies already assigned to first conformer: 1686 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MN': 2, 'ONM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MN': 2, 'ONM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG C 24 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG C 24 " occ=0.45 residue: pdb=" N AGLU C 93 " occ=0.50 ... (28 atoms not shown) pdb=" HG3BGLU C 93 " occ=0.50 residue: pdb=" N AARG D 24 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG D 24 " occ=0.45 residue: pdb=" N AGLU D 93 " occ=0.50 ... (28 atoms not shown) pdb=" HG3BGLU D 93 " occ=0.50 residue: pdb="MN MN A 503 " occ=0.99 residue: pdb="MN MN B 503 " occ=0.99 Time building chain proxies: 12.98, per 1000 atoms: 0.86 Number of scatterers: 15144 At special positions: 0 Unit cell: (86.46, 99.66, 126.72, 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) Mn 4 24.99 S 26 16.00 P 6 15.00 O 1424 8.00 N 1312 7.00 C 4850 6.00 H 7522 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 100 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 49.9% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 42 through 68 removed outlier: 3.586A pdb=" N LEU A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 removed outlier: 3.719A pdb=" N ILE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.685A pdb=" N ASP A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.722A pdb=" N PHE A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 166 removed outlier: 5.325A pdb=" N ALA A 147 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 161 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 226 removed outlier: 3.778A pdb=" N ALA A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.879A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.732A pdb=" N SER A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 290 Processing helix chain 'A' and resid 315 through 332 Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.553A pdb=" N ARG A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 68 removed outlier: 3.586A pdb=" N LEU B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 92 removed outlier: 3.719A pdb=" N ILE B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.686A pdb=" N ASP B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.723A pdb=" N PHE B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 166 removed outlier: 5.325A pdb=" N ALA B 147 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B 161 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 226 removed outlier: 3.778A pdb=" N ALA B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.880A pdb=" N ARG B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 266 removed outlier: 3.731A pdb=" N SER B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 290 Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 390 through 396 removed outlier: 3.554A pdb=" N ARG B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 103 through 108 Processing sheet with id= A, first strand: chain 'A' and resid 245 through 247 Processing sheet with id= B, first strand: chain 'A' and resid 343 through 350 removed outlier: 3.532A pdb=" N SER A 251 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 387 through 389 removed outlier: 3.721A pdb=" N VAL A 388 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 401 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 245 through 247 Processing sheet with id= E, first strand: chain 'B' and resid 343 through 350 removed outlier: 3.532A pdb=" N SER B 251 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.722A pdb=" N VAL B 388 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 401 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= H, first strand: chain 'C' and resid 115 through 117 removed outlier: 6.430A pdb=" N ARG C 43 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TRP C 52 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'D' and resid 115 through 117 removed outlier: 6.430A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1172 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: 5.61 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7520 1.03 - 1.23: 8 1.23 - 1.42: 3266 1.42 - 1.62: 4460 1.62 - 1.81: 56 Bond restraints: 15310 Sorted by residual: bond pdb=" CA6 ONM B 501 " pdb=" NA1 ONM B 501 " ideal model delta sigma weight residual 1.476 1.428 0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" CA6 ONM A 501 " pdb=" NA1 ONM A 501 " ideal model delta sigma weight residual 1.476 1.428 0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" O1G ONM B 501 " pdb=" PG ONM B 501 " ideal model delta sigma weight residual 1.556 1.515 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" O1G ONM A 501 " pdb=" PG ONM A 501 " ideal model delta sigma weight residual 1.556 1.515 0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" CG ARG C 50 " pdb=" CD ARG C 50 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.72e+00 ... (remaining 15305 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.91: 131 104.91 - 112.25: 17491 112.25 - 119.58: 3801 119.58 - 126.91: 6077 126.91 - 134.24: 114 Bond angle restraints: 27614 Sorted by residual: angle pdb=" C1' ONM B 501 " pdb=" N9 ONM B 501 " pdb=" C8 ONM B 501 " ideal model delta sigma weight residual 111.34 124.61 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C1' ONM A 501 " pdb=" N9 ONM A 501 " pdb=" C8 ONM A 501 " ideal model delta sigma weight residual 111.34 124.61 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" N ASN D 101 " pdb=" CA ASN D 101 " pdb=" C ASN D 101 " ideal model delta sigma weight residual 108.60 113.51 -4.91 1.46e+00 4.69e-01 1.13e+01 angle pdb=" N ASN C 101 " pdb=" CA ASN C 101 " pdb=" C ASN C 101 " ideal model delta sigma weight residual 108.60 113.47 -4.87 1.46e+00 4.69e-01 1.11e+01 angle pdb=" C GLN B 174 " pdb=" CA GLN B 174 " pdb=" CB GLN B 174 " ideal model delta sigma weight residual 110.17 116.01 -5.84 1.97e+00 2.58e-01 8.79e+00 ... (remaining 27609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 6469 16.43 - 32.87: 510 32.87 - 49.30: 133 49.30 - 65.73: 64 65.73 - 82.16: 8 Dihedral angle restraints: 7184 sinusoidal: 3858 harmonic: 3326 Sorted by residual: dihedral pdb=" CA GLU D 49 " pdb=" C GLU D 49 " pdb=" N ARG D 50 " pdb=" CA ARG D 50 " ideal model delta harmonic sigma weight residual -180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLU C 49 " pdb=" C GLU C 49 " pdb=" N ARG C 50 " pdb=" CA ARG C 50 " ideal model delta harmonic sigma weight residual 180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PHE A 363 " pdb=" C PHE A 363 " pdb=" N TYR A 364 " pdb=" CA TYR A 364 " ideal model delta harmonic sigma weight residual 180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 819 0.029 - 0.057: 228 0.057 - 0.086: 115 0.086 - 0.115: 52 0.115 - 0.144: 18 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA ILE A 386 " pdb=" N ILE A 386 " pdb=" C ILE A 386 " pdb=" CB ILE A 386 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE B 386 " pdb=" N ILE B 386 " pdb=" C ILE B 386 " pdb=" CB ILE B 386 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL A 366 " pdb=" N VAL A 366 " pdb=" C VAL A 366 " pdb=" CB VAL A 366 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1229 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 50 " -0.352 9.50e-02 1.11e+02 1.18e-01 1.53e+01 pdb=" NE ARG C 50 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 50 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 50 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 50 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG C 50 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 50 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG C 50 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 50 " -0.349 9.50e-02 1.11e+02 1.17e-01 1.51e+01 pdb=" NE ARG D 50 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 50 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 50 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 50 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG D 50 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG D 50 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG D 50 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 50 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 78 " -0.018 2.00e-02 2.50e+03 2.13e-02 6.80e+00 pdb=" CG ASN D 78 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN D 78 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN D 78 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN D 78 " -0.004 2.00e-02 2.50e+03 pdb="HD22 ASN D 78 " -0.026 2.00e-02 2.50e+03 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 914 2.20 - 2.80: 30546 2.80 - 3.40: 40245 3.40 - 4.00: 50957 4.00 - 4.60: 78778 Nonbonded interactions: 201440 Sorted by model distance: nonbonded pdb=" OE1 GLU B 262 " pdb=" H GLU B 262 " model vdw 1.602 1.850 nonbonded pdb=" OE1 GLU A 262 " pdb=" H GLU A 262 " model vdw 1.602 1.850 nonbonded pdb="HE22 GLN A 127 " pdb=" OE1 GLU A 164 " model vdw 1.603 1.850 nonbonded pdb="HE22 GLN B 127 " pdb=" OE1 GLU B 164 " model vdw 1.604 1.850 nonbonded pdb=" O PRO B 91 " pdb=" HD1 HIS B 94 " model vdw 1.605 1.850 ... (remaining 201435 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' and (resid 41 through 365 or resid 367 through 428 or resid 501 throu \ gh 503)) selection = (chain 'B' and (resid 41 through 365 or resid 367 through 428 or resid 501 throu \ gh 503)) } ncs_group { reference = (chain 'C' and (resid 6 through 23 or resid 26 through 92 or resid 95 through 12 \ 2)) selection = (chain 'D' and (resid 6 through 23 or resid 26 through 92 or resid 95 through 12 \ 2)) } 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=0.32 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.240 Extract box with map and model: 14.420 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 61.220 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.140 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:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 : 0.004 0.058 7788 Z= 0.255 Angle : 0.678 13.273 10642 Z= 0.361 Chirality : 0.040 0.144 1232 Planarity : 0.008 0.154 1354 Dihedral : 13.489 82.164 2704 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.61 % Allowed : 1.23 % Favored : 98.16 % Rotamer: Outliers : 0.77 % Allowed : 0.26 % Favored : 98.97 % 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: 0.96 (0.26), residues: 990 helix: 2.12 (0.22), residues: 486 sheet: -0.47 (0.35), residues: 170 loop : -0.99 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 419 HIS 0.003 0.001 HIS A 290 PHE 0.024 0.002 PHE B 363 TYR 0.013 0.001 TYR A 420 ARG 0.010 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.4978 time to fit residues: 99.7856 Evaluate side-chains 122 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.7009 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7788 Z= 0.286 Angle : 0.671 6.315 10642 Z= 0.354 Chirality : 0.043 0.182 1232 Planarity : 0.006 0.077 1354 Dihedral : 5.415 47.226 1100 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.25 % Favored : 97.14 % Rotamer: Outliers : 1.03 % Allowed : 8.74 % Favored : 90.23 % 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: 0.73 (0.26), residues: 990 helix: 1.69 (0.22), residues: 492 sheet: 0.17 (0.37), residues: 146 loop : -1.13 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 111 HIS 0.003 0.001 HIS A 315 PHE 0.018 0.002 PHE A 283 TYR 0.015 0.002 TYR C 99 ARG 0.004 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.135 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: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 135 average time/residue: 0.5387 time to fit residues: 93.8543 Evaluate side-chains 116 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7004 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7788 Z= 0.193 Angle : 0.537 6.440 10642 Z= 0.288 Chirality : 0.039 0.170 1232 Planarity : 0.005 0.070 1354 Dihedral : 5.060 43.674 1100 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.15 % Favored : 97.24 % Rotamer: Outliers : 0.90 % Allowed : 11.31 % Favored : 87.79 % 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: 1.03 (0.26), residues: 990 helix: 1.96 (0.23), residues: 492 sheet: 0.49 (0.38), residues: 146 loop : -1.09 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.001 0.000 HIS A 94 PHE 0.016 0.001 PHE B 82 TYR 0.011 0.001 TYR D 42 ARG 0.007 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ILE cc_start: 0.8360 (mm) cc_final: 0.7924 (mp) REVERT: B 422 ILE cc_start: 0.8375 (mm) cc_final: 0.7935 (mp) outliers start: 3 outliers final: 2 residues processed: 117 average time/residue: 0.5146 time to fit residues: 78.2331 Evaluate side-chains 113 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 365 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7056 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7788 Z= 0.229 Angle : 0.558 6.411 10642 Z= 0.299 Chirality : 0.041 0.192 1232 Planarity : 0.005 0.068 1354 Dihedral : 4.953 44.687 1100 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.45 % Favored : 96.93 % Rotamer: Outliers : 1.80 % Allowed : 12.47 % Favored : 85.73 % 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: 0.92 (0.26), residues: 990 helix: 1.83 (0.23), residues: 492 sheet: 0.68 (0.38), residues: 146 loop : -1.23 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 419 HIS 0.001 0.000 HIS A 315 PHE 0.016 0.002 PHE A 82 TYR 0.010 0.001 TYR C 42 ARG 0.003 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 123 average time/residue: 0.4990 time to fit residues: 80.5311 Evaluate side-chains 124 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7089 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7788 Z= 0.212 Angle : 0.537 6.445 10642 Z= 0.288 Chirality : 0.039 0.143 1232 Planarity : 0.005 0.062 1354 Dihedral : 4.850 42.926 1100 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.66 % Favored : 96.73 % Rotamer: Outliers : 2.06 % Allowed : 12.60 % Favored : 85.35 % 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: 0.90 (0.26), residues: 990 helix: 1.82 (0.23), residues: 492 sheet: 0.60 (0.38), residues: 166 loop : -1.30 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 111 HIS 0.001 0.001 HIS B 315 PHE 0.018 0.002 PHE B 82 TYR 0.010 0.001 TYR C 42 ARG 0.012 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5626 (mtt) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.4757 time to fit residues: 76.1211 Evaluate side-chains 118 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-dev-5288/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-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 61.7405 > 50: distance: 96 - 394: 20.611 distance: 137 - 402: 28.156 distance: 140 - 399: 27.217 distance: 168 - 371: 27.366 distance: 171 - 368: 31.525 distance: 203 - 334: 28.071 distance: 206 - 331: 25.781 distance: 296 - 307: 27.024 distance: 307 - 308: 10.893 distance: 307 - 314: 48.457 distance: 308 - 309: 37.054 distance: 308 - 311: 29.932 distance: 308 - 315: 40.805 distance: 309 - 310: 41.538 distance: 309 - 321: 29.423 distance: 311 - 312: 20.505 distance: 311 - 313: 28.612 distance: 311 - 316: 37.684 distance: 312 - 317: 41.502 distance: 313 - 318: 24.909 distance: 313 - 319: 19.505 distance: 313 - 320: 15.578 distance: 321 - 322: 6.289 distance: 321 - 326: 28.784 distance: 321 - 566: 29.778 distance: 322 - 323: 36.217 distance: 322 - 325: 39.278 distance: 322 - 327: 34.095 distance: 323 - 324: 30.464 distance: 323 - 331: 39.511 distance: 324 - 563: 29.865 distance: 325 - 328: 34.545 distance: 325 - 329: 28.027 distance: 325 - 330: 42.682 distance: 331 - 332: 40.444 distance: 331 - 338: 18.947 distance: 332 - 333: 8.666 distance: 332 - 335: 15.744 distance: 332 - 339: 5.472 distance: 333 - 334: 38.375 distance: 333 - 347: 35.441 distance: 335 - 336: 21.420 distance: 335 - 337: 13.215 distance: 335 - 340: 44.124 distance: 336 - 341: 11.671 distance: 336 - 342: 16.395 distance: 336 - 343: 23.966 distance: 337 - 344: 35.710 distance: 337 - 345: 44.659 distance: 337 - 346: 25.054 distance: 347 - 348: 10.181 distance: 347 - 359: 22.231 distance: 347 - 544: 11.498 distance: 348 - 349: 20.236 distance: 348 - 351: 25.517 distance: 348 - 360: 30.363 distance: 349 - 350: 24.757 distance: 349 - 368: 24.459 distance: 350 - 541: 27.153 distance: 351 - 352: 28.214 distance: 351 - 361: 28.306 distance: 351 - 362: 34.680 distance: 352 - 353: 19.608 distance: 352 - 354: 14.472 distance: 353 - 355: 9.810 distance: 353 - 363: 7.114 distance: 354 - 356: 6.362 distance: 354 - 364: 7.739 distance: 355 - 357: 14.841 distance: 355 - 365: 8.526 distance: 356 - 357: 11.503 distance: 356 - 366: 14.693 distance: 357 - 358: 11.272 distance: 358 - 367: 6.596 distance: 368 - 369: 11.768 distance: 368 - 380: 36.594 distance: 369 - 370: 23.061 distance: 369 - 372: 17.425 distance: 369 - 381: 36.754 distance: 370 - 371: 36.688 distance: 370 - 389: 10.178 distance: 372 - 373: 15.721 distance: 372 - 382: 23.395 distance: 372 - 383: 8.835 distance: 373 - 374: 9.329 distance: 373 - 375: 7.742 distance: 374 - 376: 11.973 distance: 374 - 384: 10.411 distance: 375 - 377: 5.870 distance: 375 - 385: 7.462 distance: 376 - 378: 13.344 distance: 376 - 386: 7.733 distance: 377 - 378: 7.357 distance: 377 - 387: 9.701 distance: 378 - 379: 4.719 distance: 379 - 388: 9.054 distance: 389 - 390: 6.410 distance: 389 - 395: 11.832 distance: 390 - 391: 30.687 distance: 390 - 393: 26.756 distance: 390 - 396: 20.015 distance: 391 - 392: 19.514 distance: 391 - 399: 27.980 distance: 393 - 394: 18.417 distance: 393 - 397: 14.461 distance: 393 - 398: 10.747 distance: 399 - 400: 31.619 distance: 399 - 407: 51.697 distance: 400 - 401: 20.492 distance: 400 - 403: 33.254 distance: 400 - 408: 18.303 distance: 401 - 402: 28.751 distance: 401 - 413: 29.193 distance: 403 - 404: 14.345 distance: 403 - 409: 36.140 distance: 403 - 410: 46.528 distance: 404 - 405: 22.883 distance: 404 - 406: 34.881 distance: 406 - 411: 14.803 distance: 413 - 414: 33.623 distance: 413 - 420: 7.144 distance: 414 - 415: 30.111 distance: 414 - 417: 28.440 distance: 414 - 421: 29.327 distance: 415 - 416: 41.631 distance: 415 - 427: 40.455 distance: 417 - 418: 10.158 distance: 417 - 419: 27.136 distance: 417 - 422: 48.882 distance: 418 - 423: 38.814 distance: 419 - 424: 6.797 distance: 419 - 425: 24.228 distance: 419 - 426: 22.006 distance: 427 - 428: 43.366 distance: 427 - 433: 19.542 distance: 428 - 429: 23.352 distance: 428 - 431: 25.084 distance: 428 - 434: 40.188 distance: 429 - 430: 30.211 distance: 429 - 441: 11.959 distance: 430 - 473: 20.792 distance: 431 - 432: 19.137 distance: 431 - 435: 17.020 distance: 431 - 436: 19.868 distance: 432 - 433: 16.006 distance: 432 - 437: 17.686 distance: 432 - 438: 10.654 distance: 433 - 439: 26.804 distance: 433 - 440: 21.690 distance: 441 - 442: 5.205 distance: 441 - 446: 32.505 distance: 442 - 443: 5.090 distance: 442 - 445: 16.619 distance: 442 - 447: 15.728 distance: 443 - 444: 9.235 distance: 443 - 451: 8.279 distance: 444 - 485: 9.994 distance: 445 - 448: 9.238 distance: 445 - 449: 13.969 distance: 445 - 450: 6.765