Starting phenix.real_space_refine on Fri Jan 17 13:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbg_37424/01_2025/8wbg_37424_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbg_37424/01_2025/8wbg_37424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbg_37424/01_2025/8wbg_37424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbg_37424/01_2025/8wbg_37424.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbg_37424/01_2025/8wbg_37424_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbg_37424/01_2025/8wbg_37424_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 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 80 5.16 5 C 6811 2.51 5 N 1947 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10854 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2759 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 1 Chain: "a" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 6.86, per 1000 atoms: 0.63 Number of scatterers: 10854 At special positions: 0 Unit cell: (109.65, 121.55, 111.35, 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 80 16.00 O 2016 8.00 N 1947 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 19.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 4.086A pdb=" N ALA A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.923A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.529A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.681A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.544A pdb=" N ASN A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.615A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 83 removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 341 through 345 removed outlier: 4.066A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.828A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA a 77 " --> pdb=" O GLY a 73 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU a 80 " --> pdb=" O ASN a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 237 through 241 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.597A pdb=" N TRP b 28 " --> pdb=" O VAL b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 removed outlier: 4.368A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN b 76 " --> pdb=" O GLU b 72 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA b 77 " --> pdb=" O GLY b 73 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.611A pdb=" N LEU b 241 " --> pdb=" O GLU b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.659A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.501A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.531A pdb=" N ASP A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU A 12 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.672A pdb=" N SER A 166 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS A 158 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.118A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.509A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.616A pdb=" N GLU A 274 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 203 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 193 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE a 323 " --> pdb=" O TRP a 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 removed outlier: 3.659A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU b 12 " --> pdb=" O ASP b 7 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.658A pdb=" N HIS B 35 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.748A pdb=" N GLU B 274 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER b 204 " --> pdb=" O ALA b 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.109A pdb=" N LYS a 33 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU a 169 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'a' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'a' and resid 284 through 287 Processing sheet with id=AB6, first strand: chain 'b' and resid 87 through 89 Processing sheet with id=AB7, first strand: chain 'b' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'b' and resid 284 through 287 removed outlier: 3.787A pdb=" N TRP b 311 " --> pdb=" O LYS b 284 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS b 313 " --> pdb=" O HIS b 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 298 through 299 removed outlier: 3.634A pdb=" N LEU b 298 " --> pdb=" O TYR b 331 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 726 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: 2.87 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3609 1.35 - 1.47: 2674 1.47 - 1.59: 4750 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 11145 Sorted by residual: bond pdb=" N VAL b 162 " pdb=" CA VAL b 162 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" N PHE b 160 " pdb=" CA PHE b 160 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.30e-02 5.92e+03 5.59e+00 bond pdb=" N ASP A 24 " pdb=" CA ASP A 24 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.42e-02 4.96e+03 5.42e+00 bond pdb=" N ASN a 207 " pdb=" CA ASN a 207 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.42e+00 ... (remaining 11140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 14516 1.32 - 2.65: 479 2.65 - 3.97: 95 3.97 - 5.29: 14 5.29 - 6.62: 2 Bond angle restraints: 15106 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 112.72 107.72 5.00 1.28e+00 6.10e-01 1.52e+01 angle pdb=" CA TRP A 28 " pdb=" C TRP A 28 " pdb=" N ARG A 29 " ideal model delta sigma weight residual 118.13 123.11 -4.98 1.28e+00 6.10e-01 1.51e+01 angle pdb=" N ILE b 242 " pdb=" CA ILE b 242 " pdb=" C ILE b 242 " ideal model delta sigma weight residual 111.48 107.94 3.54 9.40e-01 1.13e+00 1.42e+01 angle pdb=" CA ASP A 24 " pdb=" C ASP A 24 " pdb=" O ASP A 24 " ideal model delta sigma weight residual 122.27 117.95 4.32 1.16e+00 7.43e-01 1.39e+01 angle pdb=" C ASN a 207 " pdb=" CA ASN a 207 " pdb=" CB ASN a 207 " ideal model delta sigma weight residual 110.42 117.04 -6.62 1.99e+00 2.53e-01 1.11e+01 ... (remaining 15101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6135 17.60 - 35.19: 444 35.19 - 52.79: 91 52.79 - 70.39: 24 70.39 - 87.98: 7 Dihedral angle restraints: 6701 sinusoidal: 2816 harmonic: 3885 Sorted by residual: dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS b 313 " pdb=" SG CYS b 313 " pdb=" SG CYS b 316 " pdb=" CB CYS b 316 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS a 313 " pdb=" SG CYS a 313 " pdb=" SG CYS a 316 " pdb=" CB CYS a 316 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1235 0.043 - 0.085: 214 0.085 - 0.128: 126 0.128 - 0.170: 7 0.170 - 0.213: 2 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL b 162 " pdb=" N VAL b 162 " pdb=" C VAL b 162 " pdb=" CB VAL b 162 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1581 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 100 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 101 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ASP a 208 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP a 208 " 0.011 2.00e-02 2.50e+03 pdb=" N THR a 209 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN b 95 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO b 96 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO b 96 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 96 " 0.019 5.00e-02 4.00e+02 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 837 2.74 - 3.28: 10584 3.28 - 3.82: 16278 3.82 - 4.36: 20013 4.36 - 4.90: 36068 Nonbonded interactions: 83780 Sorted by model distance: nonbonded pdb=" OG SER B 322 " pdb=" NH1 ARG B 324 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG b 299 " pdb=" O THR b 301 " model vdw 2.206 3.120 nonbonded pdb=" OG SER B 61 " pdb=" OE1 GLU B 219 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU a 72 " pdb=" ND2 ASN a 76 " model vdw 2.236 3.120 nonbonded pdb=" OG SER b 322 " pdb=" NH1 ARG b 324 " model vdw 2.243 3.120 ... (remaining 83775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 130 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 130 through 352)) selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.710 Find NCS groups from input model: 0.450 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.003 0.038 11145 Z= 0.184 Angle : 0.582 6.617 15106 Z= 0.343 Chirality : 0.042 0.213 1584 Planarity : 0.004 0.047 1945 Dihedral : 13.023 87.838 4123 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.10 (0.24), residues: 1343 helix: 1.10 (0.44), residues: 148 sheet: -1.73 (0.36), residues: 225 loop : -0.78 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 232 HIS 0.004 0.001 HIS b 254 PHE 0.011 0.001 PHE A 123 TYR 0.010 0.001 TYR B 32 ARG 0.002 0.000 ARG a 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7669 (tpp80) REVERT: A 156 GLU cc_start: 0.7451 (pt0) cc_final: 0.7196 (pt0) REVERT: A 274 GLU cc_start: 0.8077 (tt0) cc_final: 0.7687 (mt-10) REVERT: a 207 ASN cc_start: 0.7381 (t0) cc_final: 0.6814 (t0) REVERT: a 208 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.6865 (t0) REVERT: a 251 LEU cc_start: 0.8657 (mp) cc_final: 0.8389 (mp) REVERT: a 315 GLU cc_start: 0.8065 (tt0) cc_final: 0.7557 (tp30) REVERT: b 67 MET cc_start: 0.6248 (tmm) cc_final: 0.6040 (tmm) REVERT: b 330 TRP cc_start: 0.6650 (m100) cc_final: 0.6196 (m-10) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2814 time to fit residues: 76.9857 Evaluate side-chains 121 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 207 ASN B 35 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN a 76 ASN a 207 ASN b 35 HIS b 269 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.207607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166175 restraints weight = 12162.389| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.25 r_work: 0.3689 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11145 Z= 0.309 Angle : 0.640 7.773 15106 Z= 0.339 Chirality : 0.046 0.178 1584 Planarity : 0.005 0.047 1945 Dihedral : 5.274 51.237 1478 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Rotamer: Outliers : 1.51 % Allowed : 7.40 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.19 (0.24), residues: 1343 helix: 1.00 (0.42), residues: 159 sheet: -1.73 (0.32), residues: 279 loop : -0.80 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP a 232 HIS 0.006 0.001 HIS b 254 PHE 0.029 0.002 PHE B 277 TYR 0.017 0.002 TYR a 331 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6527 (t0) cc_final: 0.6306 (t0) REVERT: A 97 MET cc_start: 0.8516 (mtm) cc_final: 0.8223 (mtt) REVERT: A 274 GLU cc_start: 0.8188 (tt0) cc_final: 0.7332 (mt-10) REVERT: A 333 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5661 (mtp) REVERT: B 339 LYS cc_start: 0.7342 (pttm) cc_final: 0.6801 (ptmm) REVERT: a 69 ARG cc_start: 0.7098 (ptp-170) cc_final: 0.6686 (tpp80) REVERT: a 146 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7795 (mmtt) REVERT: b 67 MET cc_start: 0.5883 (tmm) cc_final: 0.5596 (tmm) outliers start: 18 outliers final: 14 residues processed: 147 average time/residue: 0.2642 time to fit residues: 53.9209 Evaluate side-chains 130 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168085 restraints weight = 12321.230| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.26 r_work: 0.3714 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11145 Z= 0.211 Angle : 0.578 11.226 15106 Z= 0.302 Chirality : 0.043 0.236 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.655 19.990 1476 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 2.02 % Allowed : 9.34 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.09 (0.24), residues: 1343 helix: 1.16 (0.42), residues: 159 sheet: -1.61 (0.31), residues: 293 loop : -0.74 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 311 HIS 0.004 0.001 HIS b 254 PHE 0.021 0.001 PHE B 277 TYR 0.014 0.001 TYR A 331 ARG 0.005 0.000 ARG a 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8432 (mtm) cc_final: 0.8093 (mtt) REVERT: A 156 GLU cc_start: 0.7401 (pt0) cc_final: 0.7095 (pt0) REVERT: A 333 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5869 (mtp) REVERT: B 54 ILE cc_start: 0.6351 (mp) cc_final: 0.6117 (mp) REVERT: B 263 GLN cc_start: 0.7267 (mp10) cc_final: 0.6914 (mt0) REVERT: B 333 MET cc_start: 0.6763 (mtt) cc_final: 0.6311 (mtm) REVERT: B 339 LYS cc_start: 0.7276 (pttm) cc_final: 0.6854 (ptmm) REVERT: a 146 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7859 (mmtt) REVERT: a 324 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.8199 (mmt-90) REVERT: b 67 MET cc_start: 0.5898 (tmm) cc_final: 0.5607 (tmm) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.2553 time to fit residues: 51.2462 Evaluate side-chains 133 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8338 > 50: distance: 38 - 43: 34.227 distance: 43 - 44: 57.416 distance: 44 - 45: 58.036 distance: 44 - 47: 51.882 distance: 45 - 46: 14.261 distance: 45 - 50: 56.394 distance: 47 - 48: 59.526 distance: 47 - 49: 25.898 distance: 50 - 51: 55.420 distance: 51 - 52: 67.158 distance: 52 - 53: 57.579 distance: 52 - 54: 64.054 distance: 54 - 55: 50.578 distance: 55 - 56: 65.168 distance: 55 - 58: 68.456 distance: 56 - 57: 40.988 distance: 56 - 60: 32.132 distance: 58 - 59: 67.449 distance: 60 - 61: 15.513 distance: 61 - 62: 40.502 distance: 61 - 64: 48.322 distance: 62 - 63: 64.887 distance: 62 - 67: 39.692 distance: 64 - 65: 36.462 distance: 64 - 66: 27.229 distance: 67 - 68: 46.479 distance: 68 - 69: 59.414 distance: 68 - 71: 55.672 distance: 69 - 70: 17.631 distance: 69 - 76: 27.730 distance: 71 - 72: 51.396 distance: 72 - 73: 21.100 distance: 73 - 74: 6.591 distance: 74 - 75: 27.740 distance: 76 - 77: 68.310 distance: 77 - 78: 31.963 distance: 77 - 80: 60.322 distance: 78 - 79: 46.194 distance: 78 - 84: 64.635 distance: 80 - 81: 44.448 distance: 81 - 82: 39.652 distance: 81 - 83: 49.966 distance: 84 - 85: 57.755 distance: 85 - 86: 52.698 distance: 85 - 88: 19.860 distance: 86 - 87: 45.936 distance: 86 - 91: 20.537 distance: 88 - 89: 36.970 distance: 89 - 90: 56.539 distance: 91 - 92: 35.754 distance: 92 - 93: 9.242 distance: 92 - 95: 40.293 distance: 93 - 94: 30.914 distance: 93 - 99: 22.927 distance: 95 - 96: 28.355 distance: 96 - 97: 21.548 distance: 97 - 98: 18.647 distance: 99 - 100: 25.786 distance: 100 - 101: 37.482 distance: 100 - 103: 40.319 distance: 101 - 102: 41.976 distance: 101 - 113: 26.438 distance: 103 - 104: 14.327 distance: 104 - 105: 46.953 distance: 104 - 106: 31.914 distance: 105 - 107: 13.360 distance: 106 - 108: 16.237 distance: 106 - 109: 5.565 distance: 107 - 108: 7.590 distance: 108 - 110: 17.876 distance: 109 - 111: 6.549 distance: 110 - 112: 28.210 distance: 111 - 112: 21.778 distance: 113 - 114: 46.957 distance: 114 - 115: 40.791 distance: 114 - 117: 62.400 distance: 115 - 116: 64.757 distance: 115 - 124: 34.458 distance: 117 - 118: 47.225 distance: 118 - 119: 37.764 distance: 119 - 120: 28.986 distance: 120 - 121: 5.691 distance: 121 - 122: 11.429 distance: 121 - 123: 10.720