Starting phenix.real_space_refine on Tue Jan 14 17:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzg_38795/01_2025/8xzg_38795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzg_38795/01_2025/8xzg_38795.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/8xzg_38795/01_2025/8xzg_38795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzg_38795/01_2025/8xzg_38795.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzg_38795/01_2025/8xzg_38795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzg_38795/01_2025/8xzg_38795.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= -0.000 sd= 0.013 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 61 5.16 5 C 4572 2.51 5 N 1222 2.21 5 O 1317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 7172 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1737 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2528 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2356 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.03, per 1000 atoms: 0.56 Number of scatterers: 7172 At special positions: 0 Unit cell: (78.078, 120.666, 118.638, 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 61 16.00 O 1317 8.00 N 1222 7.00 C 4572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.02 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 44.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.941A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.524A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.114A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.509A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.019A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.703A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.899A 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 3 through 24 Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.717A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 27 through 53 Proline residue: R 32 - end of helix removed outlier: 3.942A pdb=" N GLY R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 81 removed outlier: 3.841A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 90 removed outlier: 3.517A pdb=" N TYR R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 132 removed outlier: 4.168A pdb=" N SER R 106 " --> pdb=" O CYS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 144 removed outlier: 3.859A pdb=" N ARG R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 161 Processing helix chain 'R' and resid 162 through 165 Processing helix chain 'R' and resid 190 through 192 No H-bonds generated for 'chain 'R' and resid 190 through 192' Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.522A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 240 through 275 removed outlier: 4.072A pdb=" N ARG R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU R 246 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET R 262 " --> pdb=" O ALA R 258 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 283 through 298 Proline residue: R 292 - end of helix removed outlier: 4.224A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'R' and resid 313 through 327 removed outlier: 3.739A pdb=" N ARG R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY R 327 " --> pdb=" O MET R 323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.819A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.690A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.844A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 5.969A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.576A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.543A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.845A 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: 6.691A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 168 through 172 removed outlier: 3.533A pdb=" N THR R 169 " --> pdb=" O TYR R 182 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR R 182 " --> pdb=" O THR R 169 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 957 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: 2.00 Time building geometry restraints manager: 2.02 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: 2259 1.34 - 1.45: 1178 1.45 - 1.57: 3794 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7319 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N TRP R 279 " pdb=" CA TRP R 279 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N ILE R 290 " pdb=" CA ILE R 290 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.09e-02 8.42e+03 1.23e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.12e+00 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 9516 2.02 - 4.05: 355 4.05 - 6.07: 34 6.07 - 8.09: 6 8.09 - 10.11: 1 Bond angle restraints: 9912 Sorted by residual: angle pdb=" N HIS R 231 " pdb=" CA HIS R 231 " pdb=" C HIS R 231 " ideal model delta sigma weight residual 111.36 117.00 -5.64 1.09e+00 8.42e-01 2.68e+01 angle pdb=" N THR R 99 " pdb=" CA THR R 99 " pdb=" C THR R 99 " ideal model delta sigma weight residual 111.71 105.87 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" O ILE R 31 " pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 120.42 123.50 -3.08 6.40e-01 2.44e+00 2.31e+01 angle pdb=" N LYS R 242 " pdb=" CA LYS R 242 " pdb=" C LYS R 242 " ideal model delta sigma weight residual 113.17 107.68 5.49 1.26e+00 6.30e-01 1.90e+01 angle pdb=" C TRP R 279 " pdb=" N PRO R 280 " pdb=" CA PRO R 280 " ideal model delta sigma weight residual 119.84 124.99 -5.15 1.25e+00 6.40e-01 1.70e+01 ... (remaining 9907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3844 17.18 - 34.36: 419 34.36 - 51.53: 69 51.53 - 68.71: 7 68.71 - 85.89: 4 Dihedral angle restraints: 4343 sinusoidal: 1669 harmonic: 2674 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA PHE B 241 " pdb=" C PHE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 834 0.054 - 0.108: 226 0.108 - 0.162: 62 0.162 - 0.216: 12 0.216 - 0.270: 1 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CA HIS R 231 " pdb=" N HIS R 231 " pdb=" C HIS R 231 " pdb=" CB HIS R 231 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU R 71 " pdb=" N LEU R 71 " pdb=" C LEU R 71 " pdb=" CB LEU R 71 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1132 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 230 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLY R 230 " -0.056 2.00e-02 2.50e+03 pdb=" O GLY R 230 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS R 231 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 60 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ALA B 60 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 60 " -0.018 2.00e-02 2.50e+03 pdb=" N MET B 61 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 83 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C ASP B 83 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 83 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 84 " 0.012 2.00e-02 2.50e+03 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 433 2.72 - 3.26: 6935 3.26 - 3.81: 10928 3.81 - 4.35: 13336 4.35 - 4.90: 23771 Nonbonded interactions: 55403 Sorted by model distance: nonbonded pdb=" ND2 ASN R 46 " pdb=" OD2 ASP R 75 " model vdw 2.173 3.120 nonbonded pdb=" O THR R 295 " pdb=" CE1 TYR R 299 " model vdw 2.209 3.340 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.279 3.120 ... (remaining 55398 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: 0.370 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 7319 Z= 0.514 Angle : 0.881 10.115 9912 Z= 0.580 Chirality : 0.055 0.270 1135 Planarity : 0.005 0.047 1247 Dihedral : 14.038 85.891 2606 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 1.56 % Allowed : 9.08 % Favored : 89.36 % 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: -2.72 (0.25), residues: 900 helix: -0.45 (0.25), residues: 382 sheet: -3.04 (0.29), residues: 169 loop : -2.59 (0.28), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE G 61 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.783 Fit side-chains REVERT: A 35 LYS cc_start: 0.7726 (mttt) cc_final: 0.7488 (mttp) REVERT: A 251 ASP cc_start: 0.8791 (t70) cc_final: 0.8575 (t0) REVERT: A 260 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (t) REVERT: B 118 ASP cc_start: 0.7505 (t0) cc_final: 0.7245 (t0) REVERT: B 129 ARG cc_start: 0.7139 (tpt90) cc_final: 0.6346 (mtp-110) REVERT: B 214 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6712 (mmt180) REVERT: B 226 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7847 (mt-10) REVERT: R 31 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4547 (mm) REVERT: R 323 MET cc_start: 0.6677 (mmm) cc_final: 0.5828 (mtt) outliers start: 12 outliers final: 3 residues processed: 120 average time/residue: 0.2620 time to fit residues: 39.7274 Evaluate side-chains 91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 244 HIS B 91 HIS B 155 ASN B 183 HIS G 24 ASN L 7 HIS ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 289 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.183786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134625 restraints weight = 7524.219| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.40 r_work: 0.3366 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7319 Z= 0.188 Angle : 0.553 6.012 9912 Z= 0.293 Chirality : 0.042 0.147 1135 Planarity : 0.004 0.045 1247 Dihedral : 5.120 50.435 999 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.69 % Allowed : 13.23 % Favored : 85.08 % 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: -1.46 (0.27), residues: 900 helix: 0.62 (0.27), residues: 397 sheet: -2.55 (0.31), residues: 179 loop : -1.91 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 95 HIS 0.005 0.001 HIS B 91 PHE 0.025 0.001 PHE R 39 TYR 0.012 0.001 TYR R 35 ARG 0.006 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.847 Fit side-chains REVERT: B 118 ASP cc_start: 0.8029 (t0) cc_final: 0.7768 (t0) REVERT: B 129 ARG cc_start: 0.7199 (tpt90) cc_final: 0.6038 (mtp-110) REVERT: B 152 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8128 (tt) REVERT: B 200 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8253 (m) REVERT: B 214 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6884 (mmt180) REVERT: B 226 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8390 (mt-10) REVERT: B 234 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: B 258 ASP cc_start: 0.6715 (t70) cc_final: 0.5975 (t70) REVERT: R 323 MET cc_start: 0.6652 (mmm) cc_final: 0.5860 (mtt) outliers start: 13 outliers final: 9 residues processed: 97 average time/residue: 0.2298 time to fit residues: 29.3175 Evaluate side-chains 88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 46 ASN R 231 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135077 restraints weight = 7655.215| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.51 r_work: 0.3360 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7319 Z= 0.173 Angle : 0.491 5.392 9912 Z= 0.258 Chirality : 0.041 0.142 1135 Planarity : 0.004 0.040 1247 Dihedral : 4.450 48.998 994 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.46 % Allowed : 15.18 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 900 helix: 1.02 (0.27), residues: 402 sheet: -2.39 (0.32), residues: 186 loop : -1.51 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.019 0.001 PHE R 39 TYR 0.007 0.001 TYR R 35 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.910 Fit side-chains REVERT: A 306 GLN cc_start: 0.7506 (tp40) cc_final: 0.7247 (tp40) REVERT: B 129 ARG cc_start: 0.7132 (tpt90) cc_final: 0.5988 (mtp-110) REVERT: B 152 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8094 (tt) REVERT: B 163 ASP cc_start: 0.7155 (t0) cc_final: 0.6724 (t0) REVERT: B 200 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8125 (m) REVERT: B 214 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6852 (mmt180) REVERT: B 226 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 234 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: B 258 ASP cc_start: 0.6521 (t70) cc_final: 0.5761 (t70) REVERT: R 113 MET cc_start: 0.6643 (ttp) cc_final: 0.6409 (tmm) REVERT: R 323 MET cc_start: 0.6538 (mmm) cc_final: 0.5777 (mtt) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 0.2287 time to fit residues: 31.9971 Evaluate side-chains 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.182534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131590 restraints weight = 7661.400| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.54 r_work: 0.3322 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7319 Z= 0.261 Angle : 0.521 5.613 9912 Z= 0.274 Chirality : 0.042 0.141 1135 Planarity : 0.004 0.044 1247 Dihedral : 4.415 47.279 994 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.11 % Allowed : 17.90 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.28), residues: 900 helix: 1.08 (0.27), residues: 408 sheet: -2.28 (0.33), residues: 180 loop : -1.41 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 231 PHE 0.017 0.001 PHE R 39 TYR 0.010 0.001 TYR B 105 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.795 Fit side-chains REVERT: B 129 ARG cc_start: 0.7157 (tpt90) cc_final: 0.6017 (mtp-110) REVERT: B 163 ASP cc_start: 0.7473 (t0) cc_final: 0.7217 (t0) REVERT: B 200 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8203 (m) REVERT: B 214 ARG cc_start: 0.7859 (mtt180) cc_final: 0.6900 (mmt180) REVERT: B 226 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 234 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: B 258 ASP cc_start: 0.6585 (t70) cc_final: 0.5806 (t70) REVERT: R 91 ARG cc_start: 0.3704 (OUTLIER) cc_final: 0.3190 (ptp-170) REVERT: R 113 MET cc_start: 0.6759 (ttp) cc_final: 0.6522 (tmm) REVERT: R 323 MET cc_start: 0.6558 (mmm) cc_final: 0.5775 (mtt) outliers start: 24 outliers final: 16 residues processed: 106 average time/residue: 0.2148 time to fit residues: 29.9079 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.185828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135944 restraints weight = 7603.715| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.54 r_work: 0.3350 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7319 Z= 0.174 Angle : 0.483 6.938 9912 Z= 0.251 Chirality : 0.040 0.164 1135 Planarity : 0.003 0.039 1247 Dihedral : 3.931 18.977 992 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 18.81 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.29), residues: 900 helix: 1.33 (0.27), residues: 407 sheet: -1.99 (0.34), residues: 182 loop : -1.33 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS L 7 PHE 0.014 0.001 PHE R 39 TYR 0.007 0.001 TYR R 35 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.712 Fit side-chains REVERT: A 24 ARG cc_start: 0.6873 (ttp80) cc_final: 0.6606 (ttp-110) REVERT: B 129 ARG cc_start: 0.7107 (tpt90) cc_final: 0.6005 (mtp-110) REVERT: B 163 ASP cc_start: 0.7377 (t0) cc_final: 0.7103 (t0) REVERT: B 200 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8091 (m) REVERT: B 214 ARG cc_start: 0.7826 (mtt180) cc_final: 0.6883 (mmt180) REVERT: B 217 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7513 (mtm) REVERT: B 226 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 234 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: B 258 ASP cc_start: 0.6623 (t70) cc_final: 0.5864 (t70) REVERT: R 91 ARG cc_start: 0.3627 (OUTLIER) cc_final: 0.3128 (ptp-170) REVERT: R 183 MET cc_start: 0.7297 (mtp) cc_final: 0.7089 (ttm) REVERT: R 187 MET cc_start: 0.3836 (mmm) cc_final: 0.3512 (ttm) REVERT: R 323 MET cc_start: 0.6486 (mmm) cc_final: 0.5654 (mtt) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.2266 time to fit residues: 31.3366 Evaluate side-chains 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 109 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133291 restraints weight = 7594.337| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.53 r_work: 0.3323 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7319 Z= 0.247 Angle : 0.511 7.746 9912 Z= 0.265 Chirality : 0.042 0.139 1135 Planarity : 0.004 0.043 1247 Dihedral : 3.999 19.466 992 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.50 % Allowed : 19.58 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 900 helix: 1.31 (0.27), residues: 408 sheet: -1.93 (0.35), residues: 183 loop : -1.30 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE R 39 TYR 0.008 0.001 TYR B 105 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.957 Fit side-chains REVERT: B 129 ARG cc_start: 0.7175 (tpt90) cc_final: 0.6040 (mtp85) REVERT: B 163 ASP cc_start: 0.7484 (t0) cc_final: 0.7259 (t0) REVERT: B 200 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8214 (m) REVERT: B 214 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6906 (mmt180) REVERT: B 217 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7459 (mtm) REVERT: B 226 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 234 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: B 258 ASP cc_start: 0.6570 (t70) cc_final: 0.6277 (t70) REVERT: R 91 ARG cc_start: 0.3673 (OUTLIER) cc_final: 0.3187 (ptp-170) REVERT: R 183 MET cc_start: 0.7286 (mtp) cc_final: 0.6995 (ttm) REVERT: R 187 MET cc_start: 0.3773 (mmm) cc_final: 0.3462 (ttm) REVERT: R 242 LYS cc_start: 0.8046 (mmtt) cc_final: 0.6604 (mtmt) REVERT: R 323 MET cc_start: 0.6522 (mmm) cc_final: 0.5660 (mtt) outliers start: 27 outliers final: 19 residues processed: 108 average time/residue: 0.2400 time to fit residues: 33.6795 Evaluate side-chains 113 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.183713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133702 restraints weight = 7586.462| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.49 r_work: 0.3333 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7319 Z= 0.234 Angle : 0.504 7.269 9912 Z= 0.261 Chirality : 0.041 0.138 1135 Planarity : 0.004 0.042 1247 Dihedral : 3.970 19.278 992 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.63 % Allowed : 19.71 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 900 helix: 1.40 (0.27), residues: 408 sheet: -1.84 (0.34), residues: 190 loop : -1.22 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 PHE 0.013 0.001 PHE R 39 TYR 0.013 0.001 TYR A 287 ARG 0.008 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.822 Fit side-chains REVERT: B 129 ARG cc_start: 0.7169 (tpt90) cc_final: 0.6042 (mtp85) REVERT: B 163 ASP cc_start: 0.7409 (t0) cc_final: 0.7168 (t0) REVERT: B 200 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 214 ARG cc_start: 0.7775 (mtt180) cc_final: 0.6799 (mmt180) REVERT: B 217 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7429 (mtm) REVERT: B 226 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 234 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: B 258 ASP cc_start: 0.6490 (t70) cc_final: 0.6200 (t70) REVERT: R 91 ARG cc_start: 0.3653 (OUTLIER) cc_final: 0.3193 (ptp-170) REVERT: R 183 MET cc_start: 0.7254 (mtp) cc_final: 0.6961 (ttm) REVERT: R 187 MET cc_start: 0.3643 (mmm) cc_final: 0.3341 (ttm) REVERT: R 242 LYS cc_start: 0.8006 (mmtt) cc_final: 0.6600 (mtmt) REVERT: R 323 MET cc_start: 0.6499 (mmm) cc_final: 0.5625 (mtt) outliers start: 28 outliers final: 21 residues processed: 106 average time/residue: 0.2594 time to fit residues: 35.5340 Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 72.6399 > 50: distance: 20 - 224: 31.955 distance: 23 - 221: 32.575 distance: 137 - 172: 34.140 distance: 147 - 163: 32.090 distance: 150 - 160: 34.486 distance: 155 - 160: 34.518 distance: 160 - 161: 50.326 distance: 161 - 162: 9.502 distance: 161 - 164: 21.804 distance: 162 - 163: 57.472 distance: 165 - 166: 24.569 distance: 165 - 232: 55.237 distance: 166 - 167: 52.136 distance: 166 - 169: 44.816 distance: 167 - 168: 41.841 distance: 167 - 172: 51.417 distance: 168 - 229: 62.592 distance: 169 - 171: 39.322 distance: 172 - 173: 52.012 distance: 173 - 174: 48.499 distance: 174 - 175: 57.295 distance: 174 - 176: 30.154 distance: 176 - 177: 39.043 distance: 177 - 178: 55.234 distance: 177 - 180: 41.942 distance: 178 - 179: 70.150 distance: 180 - 181: 39.232 distance: 183 - 184: 57.311 distance: 183 - 186: 67.139 distance: 186 - 187: 55.940 distance: 187 - 188: 40.410 distance: 187 - 189: 31.414 distance: 188 - 190: 20.687 distance: 189 - 191: 30.791 distance: 190 - 191: 45.788 distance: 191 - 193: 56.181 distance: 192 - 194: 27.154 distance: 193 - 195: 6.628 distance: 194 - 195: 46.391 distance: 196 - 197: 39.567 distance: 197 - 198: 40.480 distance: 197 - 200: 30.723 distance: 198 - 199: 51.410 distance: 198 - 204: 53.349 distance: 200 - 201: 33.523 distance: 201 - 202: 32.791 distance: 201 - 203: 37.815 distance: 204 - 205: 6.706 distance: 205 - 206: 11.445 distance: 205 - 208: 36.903 distance: 206 - 207: 39.843 distance: 206 - 210: 47.228 distance: 210 - 211: 45.575 distance: 211 - 212: 57.991 distance: 211 - 214: 46.787 distance: 212 - 213: 55.852 distance: 212 - 221: 56.238 distance: 214 - 215: 18.368 distance: 215 - 216: 39.748 distance: 216 - 218: 18.627 distance: 217 - 219: 40.386 distance: 218 - 220: 59.005 distance: 219 - 220: 39.662 distance: 221 - 222: 67.579 distance: 222 - 223: 36.170 distance: 222 - 225: 45.811 distance: 223 - 229: 56.245 distance: 225 - 226: 58.112 distance: 226 - 227: 43.968 distance: 226 - 228: 41.896 distance: 229 - 230: 19.170 distance: 230 - 231: 60.422 distance: 230 - 233: 53.597 distance: 231 - 232: 13.670 distance: 231 - 238: 34.929 distance: 233 - 234: 64.865 distance: 234 - 235: 41.465 distance: 235 - 236: 25.819 distance: 236 - 237: 41.420