Starting phenix.real_space_refine on Thu Jan 16 03:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfy_37208/01_2025/8kfy_37208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfy_37208/01_2025/8kfy_37208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kfy_37208/01_2025/8kfy_37208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfy_37208/01_2025/8kfy_37208.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfy_37208/01_2025/8kfy_37208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfy_37208/01_2025/8kfy_37208.cif" } resolution = 3.06 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= 0.024 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 66 5.16 5 C 5754 2.51 5 N 1505 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'OXF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.88, per 1000 atoms: 0.65 Number of scatterers: 8992 At special positions: 0 Unit cell: (94.64, 120.64, 128.96, 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 66 16.00 O 1667 8.00 N 1505 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 39.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.137A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.524A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.145A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.790A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.702A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.600A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.621A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 31 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.831A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 191 through 205 removed outlier: 3.799A pdb=" N LYS R 195 " --> pdb=" O THR R 191 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN R 199 " --> pdb=" O LYS R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.637A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 266 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.887A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 4.003A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.266A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.813A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.093A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.194A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.810A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.534A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.405A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.616A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.528A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1353 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: 2.61 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2856 1.34 - 1.46: 2115 1.46 - 1.58: 4116 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9182 Sorted by residual: bond pdb=" CA TYR S 161 " pdb=" CB TYR S 161 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.47e-02 4.63e+03 3.61e+00 bond pdb=" C12 OXF R 601 " pdb=" O3 OXF R 601 " ideal model delta sigma weight residual 1.363 1.391 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" SD MET R 105 " pdb=" CE MET R 105 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.72e+00 bond pdb=" C MET R 105 " pdb=" O MET R 105 " ideal model delta sigma weight residual 1.237 1.224 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" CG LEU R 278 " pdb=" CD2 LEU R 278 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12284 2.01 - 4.03: 126 4.03 - 6.04: 12 6.04 - 8.05: 2 8.05 - 10.06: 1 Bond angle restraints: 12425 Sorted by residual: angle pdb=" CB MET R 105 " pdb=" CG MET R 105 " pdb=" SD MET R 105 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 angle pdb=" N THR S 198 " pdb=" CA THR S 198 " pdb=" C THR S 198 " ideal model delta sigma weight residual 113.43 109.56 3.87 1.26e+00 6.30e-01 9.45e+00 angle pdb=" CG ARG B 19 " pdb=" CD ARG B 19 " pdb=" NE ARG B 19 " ideal model delta sigma weight residual 112.00 118.59 -6.59 2.20e+00 2.07e-01 8.98e+00 angle pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta sigma weight residual 121.18 115.92 5.26 1.98e+00 2.55e-01 7.05e+00 ... (remaining 12420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4723 17.68 - 35.37: 561 35.37 - 53.05: 143 53.05 - 70.73: 16 70.73 - 88.42: 4 Dihedral angle restraints: 5447 sinusoidal: 2133 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN S 130 " pdb=" C GLN S 130 " pdb=" N ALA S 131 " pdb=" CA ALA S 131 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 969 0.036 - 0.071: 318 0.071 - 0.107: 102 0.107 - 0.142: 20 0.142 - 0.178: 5 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA PHE R 290 " pdb=" N PHE R 290 " pdb=" C PHE R 290 " pdb=" CB PHE R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL R 109 " pdb=" CA VAL R 109 " pdb=" CG1 VAL R 109 " pdb=" CG2 VAL R 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR R 291 " pdb=" CA THR R 291 " pdb=" OG1 THR R 291 " pdb=" CG2 THR R 291 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1411 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 236 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO S 224 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 105 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C MET R 105 " -0.035 2.00e-02 2.50e+03 pdb=" O MET R 105 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS R 106 " 0.012 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 251 2.70 - 3.25: 8859 3.25 - 3.80: 14802 3.80 - 4.35: 19109 4.35 - 4.90: 32205 Nonbonded interactions: 75226 Sorted by model distance: nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.155 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.249 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 3.040 ... (remaining 75221 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.590 Find NCS groups from input model: 0.110 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.034 9182 Z= 0.226 Angle : 0.537 10.063 12425 Z= 0.300 Chirality : 0.041 0.178 1414 Planarity : 0.004 0.058 1556 Dihedral : 15.791 88.418 3300 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.20 % Allowed : 25.61 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.35 (0.25), residues: 1125 helix: 2.52 (0.26), residues: 398 sheet: 0.62 (0.30), residues: 288 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.003 0.001 HIS R 292 PHE 0.021 0.001 PHE R 84 TYR 0.014 0.001 TYR B 85 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7448 (mpp) cc_final: 0.7088 (mmm) REVERT: A 349 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7578 (mtmm) REVERT: B 19 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: R 46 PHE cc_start: 0.8327 (t80) cc_final: 0.8052 (t80) REVERT: R 202 MET cc_start: 0.7523 (mmm) cc_final: 0.7200 (mtp) REVERT: S 154 LEU cc_start: 0.8196 (tp) cc_final: 0.7943 (tp) outliers start: 2 outliers final: 1 residues processed: 227 average time/residue: 0.2724 time to fit residues: 79.9133 Evaluate side-chains 223 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS S 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112957 restraints weight = 13625.025| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.21 r_work: 0.3312 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9182 Z= 0.215 Angle : 0.517 8.057 12425 Z= 0.285 Chirality : 0.042 0.194 1414 Planarity : 0.004 0.060 1556 Dihedral : 4.748 50.754 1252 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.95 % Allowed : 21.05 % Favored : 75.00 % 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: 1.51 (0.25), residues: 1125 helix: 2.69 (0.25), residues: 403 sheet: 0.63 (0.30), residues: 285 loop : -0.33 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS S 155 PHE 0.021 0.001 PHE R 214 TYR 0.016 0.001 TYR S 178 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7274 (mpp) cc_final: 0.7017 (mmm) REVERT: A 184 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 279 LYS cc_start: 0.8539 (mttt) cc_final: 0.8325 (mptt) REVERT: A 298 GLU cc_start: 0.7122 (tp30) cc_final: 0.6670 (tp30) REVERT: A 328 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6991 (m-30) REVERT: B 19 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: B 212 ASP cc_start: 0.7888 (t0) cc_final: 0.7569 (t0) REVERT: B 263 THR cc_start: 0.8250 (p) cc_final: 0.7890 (m) REVERT: B 335 PHE cc_start: 0.8471 (m-80) cc_final: 0.8025 (m-80) REVERT: R 46 PHE cc_start: 0.8269 (t80) cc_final: 0.8033 (t80) REVERT: R 124 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7879 (mm) REVERT: R 202 MET cc_start: 0.7805 (mmm) cc_final: 0.7551 (mtp) REVERT: R 215 MET cc_start: 0.7910 (mmm) cc_final: 0.7385 (mpp) REVERT: R 257 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8077 (p) REVERT: S 34 MET cc_start: 0.8193 (mmm) cc_final: 0.7975 (mmm) REVERT: S 154 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7763 (tp) REVERT: S 160 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8381 (m) outliers start: 39 outliers final: 23 residues processed: 241 average time/residue: 0.2464 time to fit residues: 79.5164 Evaluate side-chains 240 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 142 HIS R 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112804 restraints weight = 13807.898| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.18 r_work: 0.3311 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9182 Z= 0.207 Angle : 0.494 7.532 12425 Z= 0.271 Chirality : 0.041 0.194 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.703 51.609 1252 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.95 % Allowed : 22.27 % Favored : 73.79 % 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: 1.54 (0.25), residues: 1125 helix: 2.69 (0.25), residues: 405 sheet: 0.64 (0.30), residues: 279 loop : -0.30 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.002 0.001 HIS B 91 PHE 0.020 0.001 PHE R 214 TYR 0.026 0.002 TYR S 223 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7169 (mpp) cc_final: 0.6830 (mmm) REVERT: A 184 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 279 LYS cc_start: 0.8518 (mttt) cc_final: 0.8301 (mptt) REVERT: A 298 GLU cc_start: 0.7193 (tp30) cc_final: 0.6793 (tp30) REVERT: A 317 LYS cc_start: 0.8293 (ptpp) cc_final: 0.7564 (ptpp) REVERT: A 328 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: A 345 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7820 (mptt) REVERT: B 19 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7361 (mtm-85) REVERT: B 134 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7955 (ttp80) REVERT: B 197 ARG cc_start: 0.7402 (mpt-90) cc_final: 0.7000 (mpt-90) REVERT: B 212 ASP cc_start: 0.7932 (t0) cc_final: 0.7604 (t0) REVERT: B 335 PHE cc_start: 0.8450 (m-80) cc_final: 0.8032 (m-80) REVERT: R 46 PHE cc_start: 0.8306 (t80) cc_final: 0.8062 (t80) REVERT: R 250 PHE cc_start: 0.7409 (m-10) cc_final: 0.7134 (m-10) REVERT: R 257 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8082 (p) REVERT: S 148 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7285 (ttm170) REVERT: S 154 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7801 (tp) outliers start: 39 outliers final: 28 residues processed: 239 average time/residue: 0.2338 time to fit residues: 74.7673 Evaluate side-chains 248 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110378 restraints weight = 13669.736| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.14 r_work: 0.3292 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9182 Z= 0.290 Angle : 0.522 6.806 12425 Z= 0.286 Chirality : 0.042 0.210 1414 Planarity : 0.004 0.057 1556 Dihedral : 4.782 51.457 1252 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.06 % Allowed : 21.15 % Favored : 73.79 % 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: 1.37 (0.25), residues: 1125 helix: 2.55 (0.25), residues: 405 sheet: 0.45 (0.30), residues: 282 loop : -0.31 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.002 PHE R 214 TYR 0.023 0.002 TYR S 223 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7238 (mpp) cc_final: 0.6888 (mmm) REVERT: A 298 GLU cc_start: 0.7211 (tp30) cc_final: 0.6779 (tp30) REVERT: A 328 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: A 345 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7839 (mptt) REVERT: B 19 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7306 (mtm-85) REVERT: B 134 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7939 (ttp80) REVERT: B 178 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8435 (p) REVERT: B 197 ARG cc_start: 0.7437 (mpt-90) cc_final: 0.7033 (mpt-90) REVERT: B 212 ASP cc_start: 0.7997 (t0) cc_final: 0.7769 (m-30) REVERT: B 263 THR cc_start: 0.8293 (p) cc_final: 0.7949 (m) REVERT: B 335 PHE cc_start: 0.8459 (m-80) cc_final: 0.8038 (m-80) REVERT: R 46 PHE cc_start: 0.8337 (t80) cc_final: 0.8098 (t80) REVERT: R 257 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8084 (p) REVERT: R 278 LEU cc_start: 0.8106 (mm) cc_final: 0.7829 (mt) REVERT: S 148 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7317 (ttm170) REVERT: S 154 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7893 (tp) REVERT: S 185 SER cc_start: 0.8512 (m) cc_final: 0.8229 (p) outliers start: 50 outliers final: 37 residues processed: 252 average time/residue: 0.2637 time to fit residues: 87.5344 Evaluate side-chains 262 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 308 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110237 restraints weight = 13665.949| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.14 r_work: 0.3292 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9182 Z= 0.254 Angle : 0.510 7.130 12425 Z= 0.278 Chirality : 0.041 0.195 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.746 51.675 1252 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.06 % Allowed : 21.46 % Favored : 73.48 % 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: 1.34 (0.25), residues: 1125 helix: 2.54 (0.25), residues: 405 sheet: 0.37 (0.30), residues: 281 loop : -0.30 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.003 0.001 HIS B 142 PHE 0.022 0.002 PHE R 214 TYR 0.021 0.002 TYR S 223 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7309 (mpp) cc_final: 0.6999 (mmm) REVERT: A 298 GLU cc_start: 0.7211 (tp30) cc_final: 0.6768 (tp30) REVERT: B 19 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: B 134 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7937 (ttp80) REVERT: B 150 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7759 (mpt180) REVERT: B 197 ARG cc_start: 0.7450 (mpt-90) cc_final: 0.6966 (mpt-90) REVERT: B 251 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8475 (mtt90) REVERT: B 263 THR cc_start: 0.8315 (p) cc_final: 0.7865 (m) REVERT: B 335 PHE cc_start: 0.8444 (m-80) cc_final: 0.8048 (m-80) REVERT: R 46 PHE cc_start: 0.8396 (t80) cc_final: 0.8133 (t80) REVERT: R 103 THR cc_start: 0.8065 (p) cc_final: 0.7712 (t) REVERT: R 257 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8094 (p) REVERT: R 278 LEU cc_start: 0.8189 (mm) cc_final: 0.7889 (mt) REVERT: S 78 THR cc_start: 0.8279 (t) cc_final: 0.8013 (p) REVERT: S 148 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7304 (ttm170) REVERT: S 154 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7901 (tp) REVERT: S 185 SER cc_start: 0.8503 (m) cc_final: 0.8208 (p) outliers start: 50 outliers final: 36 residues processed: 249 average time/residue: 0.2550 time to fit residues: 83.7452 Evaluate side-chains 265 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 308 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.131159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111240 restraints weight = 13704.019| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.15 r_work: 0.3290 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9182 Z= 0.251 Angle : 0.510 6.475 12425 Z= 0.279 Chirality : 0.042 0.204 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.747 51.516 1252 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.45 % Allowed : 21.36 % Favored : 74.19 % 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: 1.29 (0.25), residues: 1125 helix: 2.52 (0.25), residues: 405 sheet: 0.30 (0.31), residues: 273 loop : -0.31 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.022 0.001 PHE R 214 TYR 0.021 0.002 TYR S 223 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7326 (mpp) cc_final: 0.7024 (mmm) REVERT: A 298 GLU cc_start: 0.7238 (tp30) cc_final: 0.6788 (tp30) REVERT: A 317 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7841 (ptpp) REVERT: B 19 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7351 (mtm-85) REVERT: B 134 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7931 (ttp80) REVERT: B 137 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7689 (tpp80) REVERT: B 150 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.7770 (mpt180) REVERT: B 197 ARG cc_start: 0.7459 (mpt-90) cc_final: 0.6996 (mpt-90) REVERT: B 335 PHE cc_start: 0.8439 (m-80) cc_final: 0.8052 (m-80) REVERT: R 46 PHE cc_start: 0.8395 (t80) cc_final: 0.8122 (t80) REVERT: R 257 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8058 (p) REVERT: R 278 LEU cc_start: 0.8182 (mm) cc_final: 0.7773 (mt) REVERT: S 78 THR cc_start: 0.8270 (t) cc_final: 0.8020 (p) REVERT: S 148 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7318 (ttm170) REVERT: S 185 SER cc_start: 0.8512 (m) cc_final: 0.8210 (p) outliers start: 44 outliers final: 36 residues processed: 244 average time/residue: 0.2610 time to fit residues: 83.1272 Evaluate side-chains 258 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 308 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 70.2727 > 50: distance: 3 - 25: 25.835 distance: 7 - 31: 25.355 distance: 17 - 39: 25.921 distance: 21 - 25: 26.229 distance: 22 - 47: 33.301 distance: 25 - 26: 39.969 distance: 26 - 27: 32.491 distance: 26 - 29: 25.058 distance: 27 - 31: 44.333 distance: 28 - 51: 51.394 distance: 29 - 30: 11.710 distance: 31 - 32: 10.861 distance: 32 - 33: 5.034 distance: 32 - 35: 7.505 distance: 33 - 34: 16.654 distance: 33 - 39: 10.013 distance: 34 - 59: 57.798 distance: 35 - 36: 31.350 distance: 36 - 37: 19.707 distance: 36 - 38: 23.286 distance: 39 - 40: 7.280 distance: 40 - 41: 17.992 distance: 40 - 43: 14.182 distance: 41 - 42: 4.519 distance: 41 - 47: 3.548 distance: 42 - 65: 47.635 distance: 43 - 44: 10.306 distance: 44 - 45: 27.234 distance: 44 - 46: 19.701 distance: 47 - 48: 18.729 distance: 48 - 49: 27.893 distance: 49 - 50: 26.760 distance: 49 - 51: 39.502 distance: 50 - 73: 8.448 distance: 51 - 52: 28.337 distance: 52 - 53: 15.949 distance: 52 - 55: 28.789 distance: 53 - 54: 15.366 distance: 53 - 59: 12.372 distance: 54 - 80: 51.272 distance: 56 - 57: 39.886 distance: 60 - 61: 4.094 distance: 60 - 63: 27.697 distance: 61 - 65: 14.046 distance: 62 - 88: 5.055 distance: 63 - 64: 37.201 distance: 65 - 66: 26.452 distance: 66 - 67: 54.106 distance: 66 - 69: 8.280 distance: 67 - 68: 22.505 distance: 67 - 73: 8.230 distance: 68 - 96: 24.409 distance: 69 - 70: 16.197 distance: 70 - 71: 37.143 distance: 70 - 72: 10.951 distance: 73 - 74: 22.030 distance: 74 - 75: 50.572 distance: 74 - 77: 27.788 distance: 75 - 76: 5.687 distance: 75 - 80: 35.091 distance: 76 - 103: 33.084 distance: 77 - 78: 40.341 distance: 80 - 81: 50.719 distance: 81 - 82: 8.024 distance: 81 - 84: 32.447 distance: 82 - 88: 6.422 distance: 83 - 110: 33.939 distance: 84 - 85: 8.036 distance: 84 - 86: 22.789 distance: 88 - 89: 4.247 distance: 89 - 90: 5.111 distance: 89 - 92: 4.063 distance: 90 - 91: 47.348 distance: 90 - 96: 34.506 distance: 91 - 115: 27.201