Starting phenix.real_space_refine on Mon Aug 25 00:10:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gao_29902/08_2025/8gao_29902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gao_29902/08_2025/8gao_29902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2025/8gao_29902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2025/8gao_29902.map" model { file = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2025/8gao_29902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2025/8gao_29902.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.050 sd= 0.387 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 41 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 15149 2.51 5 N 4000 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23987 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "G" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 24, 'TRANS': 314} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20839 SG CYS G 37 50.110 92.436 69.765 1.00234.26 S ATOM 20859 SG CYS G 40 46.540 91.001 70.356 1.00251.45 S ATOM 21058 SG CYS G 65 49.027 90.884 73.007 1.00220.03 S ATOM 21084 SG CYS G 68 49.610 88.675 69.955 1.00211.90 S Time building chain proxies: 6.51, per 1000 atoms: 0.27 Number of scatterers: 23987 At special positions: 0 Unit cell: (140.973, 137.886, 143.031, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 132 16.00 P 41 15.00 Mg 5 11.99 O 4659 8.00 N 4000 7.00 C 15149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 65 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 37 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 68 " Number of angles added : 6 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 18 sheets defined 54.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 removed outlier: 4.084A pdb=" N PHE A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 removed outlier: 3.718A pdb=" N LEU A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.724A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.504A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.642A pdb=" N PHE A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 375 through 381 removed outlier: 3.541A pdb=" N THR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 4.224A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.534A pdb=" N ASN B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.613A pdb=" N CYS B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.534A pdb=" N ASP B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.573A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.529A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.762A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.827A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 removed outlier: 3.558A pdb=" N LEU C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 229 through 242 removed outlier: 3.870A pdb=" N ASN C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 255 through 269 removed outlier: 3.644A pdb=" N LYS C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.731A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 4.085A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 3.728A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.749A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.504A pdb=" N ASN D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.829A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 255 through 269 removed outlier: 3.619A pdb=" N LYS D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.675A pdb=" N TRP D 361 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.764A pdb=" N PHE E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.531A pdb=" N ASN E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 119 removed outlier: 3.513A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 242 Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.516A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.770A pdb=" N TRP E 361 " --> pdb=" O LYS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.534A pdb=" N PHE F 28 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.722A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 119 removed outlier: 3.593A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.616A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 268 Processing helix chain 'F' and resid 286 through 300 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.581A pdb=" N ILE F 371 " --> pdb=" O MET F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 82 through 99 removed outlier: 3.831A pdb=" N ARG G 94 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY G 98 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 134 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 3.996A pdb=" N LYS G 151 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 235 through 240 Processing helix chain 'G' and resid 274 through 287 removed outlier: 3.677A pdb=" N ILE G 278 " --> pdb=" O HIS G 274 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 287 " --> pdb=" O LYS G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'G' and resid 328 through 341 removed outlier: 4.410A pdb=" N LYS G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.453A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN B 193 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 354 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 195 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.599A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 278 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.527A pdb=" N VAL C 277 " --> pdb=" O HIS B 152 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.650A pdb=" N ALA B 187 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AA8, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AA9, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.294A pdb=" N VAL E 221 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS E 278 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR E 223 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA E 386 " --> pdb=" O GLN E 403 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN E 403 " --> pdb=" O ALA E 386 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE E 388 " --> pdb=" O ILE E 401 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE E 401 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB2, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.937A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB4, first strand: chain 'F' and resid 350 through 352 removed outlier: 3.748A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AB6, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB7, first strand: chain 'G' and resid 23 through 27 Processing sheet with id=AB8, first strand: chain 'G' and resid 124 through 126 removed outlier: 5.270A pdb=" N LEU G 180 " --> pdb=" O GLY G 196 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY G 196 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE G 182 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE G 194 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 184 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 219 through 220 removed outlier: 3.508A pdb=" N ILE G 248 " --> pdb=" O LEU G 233 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG G 264 " --> pdb=" O ARG G 290 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET G 292 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP G 266 " --> pdb=" O MET G 292 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3363 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: 4.86 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7692 1.36 - 1.50: 6603 1.50 - 1.65: 9986 1.65 - 1.80: 141 1.80 - 1.95: 88 Bond restraints: 24510 Sorted by residual: bond pdb=" N VAL A 221 " pdb=" CA VAL A 221 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" N GLU E 188 " pdb=" CA GLU E 188 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.61e+00 bond pdb=" N ILE A 224 " pdb=" CA ILE A 224 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.08e-02 8.57e+03 8.35e+00 bond pdb=" N VAL D 199 " pdb=" CA VAL D 199 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.16e+00 bond pdb=" N LEU E 192 " pdb=" CA LEU E 192 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.63e+00 ... (remaining 24505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 32904 2.27 - 4.55: 324 4.55 - 6.82: 21 6.82 - 9.10: 10 9.10 - 11.37: 4 Bond angle restraints: 33263 Sorted by residual: angle pdb=" N LEU A 207 " pdb=" CA LEU A 207 " pdb=" C LEU A 207 " ideal model delta sigma weight residual 111.28 104.72 6.56 1.09e+00 8.42e-01 3.62e+01 angle pdb=" N PRO A 378 " pdb=" CA PRO A 378 " pdb=" C PRO A 378 " ideal model delta sigma weight residual 113.53 106.29 7.24 1.39e+00 5.18e-01 2.72e+01 angle pdb=" N VAL D 201 " pdb=" CA VAL D 201 " pdb=" C VAL D 201 " ideal model delta sigma weight residual 112.29 107.86 4.43 9.40e-01 1.13e+00 2.22e+01 angle pdb=" N LEU A 210 " pdb=" CA LEU A 210 " pdb=" C LEU A 210 " ideal model delta sigma weight residual 111.11 106.32 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" PB GTP P 1 " pdb=" O3B GTP P 1 " pdb=" PG GTP P 1 " ideal model delta sigma weight residual 120.50 131.87 -11.37 3.00e+00 1.11e-01 1.44e+01 ... (remaining 33258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14580 35.94 - 71.87: 233 71.87 - 107.81: 8 107.81 - 143.75: 0 143.75 - 179.68: 3 Dihedral angle restraints: 14824 sinusoidal: 6212 harmonic: 8612 Sorted by residual: dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 111.95 -179.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -86.76 155.67 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.57 -74.30 1 2.00e+01 2.50e-03 1.75e+01 ... (remaining 14821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2803 0.042 - 0.083: 643 0.083 - 0.125: 220 0.125 - 0.167: 27 0.167 - 0.209: 4 Chirality restraints: 3697 Sorted by residual: chirality pdb=" CA VAL E 244 " pdb=" N VAL E 244 " pdb=" C VAL E 244 " pdb=" CB VAL E 244 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE F 321 " pdb=" N ILE F 321 " pdb=" C ILE F 321 " pdb=" CB ILE F 321 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA LEU A 210 " pdb=" N LEU A 210 " pdb=" C LEU A 210 " pdb=" CB LEU A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 3694 not shown) Planarity restraints: 4105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 187 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C ALA E 187 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA E 187 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 188 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 316 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C CYS F 316 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS F 316 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS F 317 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 377 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C LEU A 377 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 377 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 378 " -0.011 2.00e-02 2.50e+03 ... (remaining 4102 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 235 2.52 - 3.11: 18826 3.11 - 3.71: 39218 3.71 - 4.30: 55372 4.30 - 4.90: 90320 Nonbonded interactions: 203971 Sorted by model distance: nonbonded pdb=" O2A AGS F 501 " pdb="MG MG F 502 " model vdw 1.924 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.932 2.170 nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.934 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 1.938 2.170 nonbonded pdb=" O3G AGS E 501 " pdb="MG MG E 502 " model vdw 1.980 2.170 ... (remaining 203966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.700 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 0.052 24515 Z= 0.182 Angle : 0.594 11.371 33269 Z= 0.355 Chirality : 0.041 0.209 3697 Planarity : 0.003 0.044 4105 Dihedral : 12.626 179.685 9262 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.47 % Allowed : 7.64 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2917 helix: 1.46 (0.14), residues: 1419 sheet: -1.24 (0.27), residues: 357 loop : -1.09 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 236 TYR 0.012 0.001 TYR E 15 PHE 0.012 0.001 PHE D 65 TRP 0.015 0.001 TRP B 162 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00304 (24510) covalent geometry : angle 0.59208 (33263) hydrogen bonds : bond 0.15156 ( 1174) hydrogen bonds : angle 6.46390 ( 3363) metal coordination : bond 0.00624 ( 4) metal coordination : angle 3.42775 ( 6) Misc. bond : bond 0.05155 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1290 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 11 PHE cc_start: 0.8133 (m-80) cc_final: 0.7603 (m-80) REVERT: A 19 VAL cc_start: 0.8366 (m) cc_final: 0.7943 (p) REVERT: A 66 THR cc_start: 0.8833 (p) cc_final: 0.8596 (p) REVERT: A 73 VAL cc_start: 0.8295 (t) cc_final: 0.7454 (p) REVERT: A 79 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7762 (ttmt) REVERT: A 85 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 103 MET cc_start: 0.8244 (mmm) cc_final: 0.7994 (mmm) REVERT: A 104 PHE cc_start: 0.8251 (t80) cc_final: 0.7575 (t80) REVERT: A 113 ILE cc_start: 0.8724 (mt) cc_final: 0.8196 (mt) REVERT: A 123 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7706 (mmmm) REVERT: A 131 VAL cc_start: 0.9071 (t) cc_final: 0.8823 (m) REVERT: A 136 ASP cc_start: 0.7389 (m-30) cc_final: 0.7169 (m-30) REVERT: A 163 LEU cc_start: 0.8984 (tp) cc_final: 0.8781 (tt) REVERT: A 164 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: A 165 TYR cc_start: 0.8497 (m-10) cc_final: 0.8221 (m-10) REVERT: A 174 PHE cc_start: 0.8449 (m-80) cc_final: 0.8138 (m-10) REVERT: A 191 THR cc_start: 0.8949 (p) cc_final: 0.8683 (p) REVERT: A 214 TYR cc_start: 0.9045 (m-10) cc_final: 0.8525 (m-10) REVERT: A 223 TYR cc_start: 0.8071 (t80) cc_final: 0.7777 (t80) REVERT: A 224 ILE cc_start: 0.8288 (mt) cc_final: 0.7834 (mt) REVERT: A 235 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7938 (ttpt) REVERT: A 241 MET cc_start: 0.8216 (mmm) cc_final: 0.7729 (mmm) REVERT: A 255 SER cc_start: 0.8355 (p) cc_final: 0.7368 (p) REVERT: A 265 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8243 (ttpp) REVERT: A 312 TYR cc_start: 0.6557 (t80) cc_final: 0.6022 (t80) REVERT: A 316 CYS cc_start: 0.8081 (m) cc_final: 0.7484 (m) REVERT: A 342 LEU cc_start: 0.8205 (tp) cc_final: 0.7290 (tp) REVERT: A 371 ILE cc_start: 0.6832 (mt) cc_final: 0.6457 (mt) REVERT: A 403 GLN cc_start: 0.7578 (tt0) cc_final: 0.7360 (tt0) REVERT: A 408 TYR cc_start: 0.8731 (m-80) cc_final: 0.8497 (m-80) REVERT: A 416 LYS cc_start: 0.8748 (mptt) cc_final: 0.8484 (mptt) REVERT: A 423 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8310 (mmmm) REVERT: B 3 GLU cc_start: 0.7653 (tt0) cc_final: 0.7067 (tt0) REVERT: B 8 HIS cc_start: 0.8300 (m90) cc_final: 0.7749 (m90) REVERT: B 47 TYR cc_start: 0.8572 (m-80) cc_final: 0.7820 (m-10) REVERT: B 70 TYR cc_start: 0.8353 (t80) cc_final: 0.8030 (t80) REVERT: B 79 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8135 (ttmm) REVERT: B 92 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8157 (mmtt) REVERT: B 101 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8277 (tpp-160) REVERT: B 103 MET cc_start: 0.7772 (mmm) cc_final: 0.7558 (mmm) REVERT: B 155 MET cc_start: 0.7612 (tpp) cc_final: 0.7130 (tpp) REVERT: B 159 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 161 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8231 (ttp-110) REVERT: B 175 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7057 (ttpp) REVERT: B 192 LEU cc_start: 0.8796 (tp) cc_final: 0.8578 (tt) REVERT: B 196 MET cc_start: 0.6887 (mtm) cc_final: 0.6381 (ptp) REVERT: B 213 ASP cc_start: 0.7889 (m-30) cc_final: 0.7631 (m-30) REVERT: B 226 MET cc_start: 0.8432 (mmm) cc_final: 0.7963 (mmp) REVERT: B 231 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 243 ASP cc_start: 0.7076 (t0) cc_final: 0.6723 (t0) REVERT: B 245 SER cc_start: 0.8913 (t) cc_final: 0.8437 (p) REVERT: B 265 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8553 (ttmt) REVERT: B 271 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7550 (t) REVERT: B 300 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7668 (mtpt) REVERT: B 318 SER cc_start: 0.7871 (m) cc_final: 0.7534 (t) REVERT: B 324 TYR cc_start: 0.7557 (t80) cc_final: 0.7320 (t80) REVERT: B 325 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7230 (p) REVERT: B 345 GLU cc_start: 0.7912 (tt0) cc_final: 0.7674 (tt0) REVERT: B 392 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 403 GLN cc_start: 0.7434 (tt0) cc_final: 0.7103 (tt0) REVERT: B 413 LYS cc_start: 0.8507 (tppt) cc_final: 0.8138 (tppt) REVERT: C 22 TYR cc_start: 0.8779 (m-80) cc_final: 0.8569 (m-10) REVERT: C 26 GLU cc_start: 0.7532 (pt0) cc_final: 0.7279 (pt0) REVERT: C 39 LEU cc_start: 0.8864 (mt) cc_final: 0.8519 (mt) REVERT: C 41 LYS cc_start: 0.8523 (tttt) cc_final: 0.8128 (tttt) REVERT: C 80 LEU cc_start: 0.7835 (mt) cc_final: 0.7583 (mp) REVERT: C 109 LYS cc_start: 0.8730 (tptt) cc_final: 0.8498 (tptt) REVERT: C 114 GLN cc_start: 0.8117 (mt0) cc_final: 0.7684 (mt0) REVERT: C 149 TYR cc_start: 0.7083 (m-10) cc_final: 0.6803 (m-10) REVERT: C 167 ASN cc_start: 0.8305 (p0) cc_final: 0.7855 (p0) REVERT: C 180 ASN cc_start: 0.8598 (m-40) cc_final: 0.8379 (m-40) REVERT: C 181 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8022 (ttpp) REVERT: C 200 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6478 (t160) REVERT: C 226 MET cc_start: 0.7847 (mmt) cc_final: 0.7595 (mmt) REVERT: C 240 ASN cc_start: 0.8067 (t0) cc_final: 0.7607 (t0) REVERT: C 241 MET cc_start: 0.8096 (mmm) cc_final: 0.7642 (mmm) REVERT: C 255 SER cc_start: 0.8313 (m) cc_final: 0.7956 (p) REVERT: C 263 MET cc_start: 0.7325 (mmm) cc_final: 0.6953 (mmm) REVERT: C 272 LEU cc_start: 0.9012 (tp) cc_final: 0.8797 (tt) REVERT: C 280 TYR cc_start: 0.8934 (m-80) cc_final: 0.8618 (m-80) REVERT: C 292 SER cc_start: 0.8802 (m) cc_final: 0.8429 (t) REVERT: C 294 LEU cc_start: 0.9206 (mt) cc_final: 0.8969 (mt) REVERT: C 322 ARG cc_start: 0.7094 (ttp-110) cc_final: 0.6869 (ttp-110) REVERT: C 331 THR cc_start: 0.8178 (m) cc_final: 0.7901 (t) REVERT: C 345 GLU cc_start: 0.7859 (tt0) cc_final: 0.7485 (tt0) REVERT: C 402 LYS cc_start: 0.7986 (pttt) cc_final: 0.7678 (ptmt) REVERT: C 416 LYS cc_start: 0.8189 (mttt) cc_final: 0.7984 (mttt) REVERT: D 11 PHE cc_start: 0.7663 (m-80) cc_final: 0.7089 (m-10) REVERT: D 19 VAL cc_start: 0.8683 (m) cc_final: 0.8066 (p) REVERT: D 40 ILE cc_start: 0.9249 (mt) cc_final: 0.9036 (mm) REVERT: D 41 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8095 (ttmm) REVERT: D 47 TYR cc_start: 0.8899 (m-80) cc_final: 0.8241 (m-80) REVERT: D 54 ASN cc_start: 0.8315 (m-40) cc_final: 0.8091 (m110) REVERT: D 89 TRP cc_start: 0.8047 (t60) cc_final: 0.7466 (t60) REVERT: D 93 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7170 (mm-30) REVERT: D 103 MET cc_start: 0.8158 (mmm) cc_final: 0.7316 (mmm) REVERT: D 109 LYS cc_start: 0.8561 (tttp) cc_final: 0.8213 (ttmm) REVERT: D 111 ILE cc_start: 0.8320 (mt) cc_final: 0.8055 (mt) REVERT: D 118 GLU cc_start: 0.7396 (tp30) cc_final: 0.6831 (tp30) REVERT: D 128 MET cc_start: 0.8694 (tpp) cc_final: 0.8348 (tpp) REVERT: D 143 SER cc_start: 0.8913 (m) cc_final: 0.7972 (t) REVERT: D 153 ASP cc_start: 0.7711 (t0) cc_final: 0.7420 (t0) REVERT: D 154 TRP cc_start: 0.8644 (t60) cc_final: 0.8319 (t60) REVERT: D 159 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6269 (tp30) REVERT: D 189 THR cc_start: 0.8617 (p) cc_final: 0.7373 (p) REVERT: D 192 LEU cc_start: 0.9168 (tp) cc_final: 0.8951 (tp) REVERT: D 226 MET cc_start: 0.7759 (mmm) cc_final: 0.7037 (mmm) REVERT: D 237 ILE cc_start: 0.8894 (mm) cc_final: 0.8417 (mm) REVERT: D 263 MET cc_start: 0.7999 (mmm) cc_final: 0.7529 (mmm) REVERT: D 264 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8126 (mm-30) REVERT: D 267 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7574 (ttm-80) REVERT: D 280 TYR cc_start: 0.8401 (m-80) cc_final: 0.8072 (m-80) REVERT: D 324 TYR cc_start: 0.7427 (m-80) cc_final: 0.7139 (m-80) REVERT: D 326 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7364 (mm-30) REVERT: D 347 GLU cc_start: 0.7136 (tp30) cc_final: 0.6711 (tp30) REVERT: D 392 GLU cc_start: 0.7163 (tp30) cc_final: 0.6819 (tp30) REVERT: D 393 LEU cc_start: 0.8343 (mt) cc_final: 0.8049 (mm) REVERT: D 412 ASN cc_start: 0.8017 (m-40) cc_final: 0.7797 (m-40) REVERT: D 414 TRP cc_start: 0.8324 (m-90) cc_final: 0.8047 (m100) REVERT: D 425 ASN cc_start: 0.8433 (m110) cc_final: 0.8056 (m-40) REVERT: E 4 ILE cc_start: 0.8944 (mt) cc_final: 0.8669 (mt) REVERT: E 35 ASN cc_start: 0.8008 (m-40) cc_final: 0.7414 (m-40) REVERT: E 38 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8459 (mtpt) REVERT: E 39 LEU cc_start: 0.8766 (mt) cc_final: 0.8460 (mt) REVERT: E 104 PHE cc_start: 0.8585 (t80) cc_final: 0.8072 (t80) REVERT: E 127 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8250 (ttmt) REVERT: E 144 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7277 (tt) REVERT: E 158 TYR cc_start: 0.6134 (p90) cc_final: 0.5286 (p90) REVERT: E 216 GLN cc_start: 0.7671 (mt0) cc_final: 0.7394 (mt0) REVERT: E 237 ILE cc_start: 0.8656 (mt) cc_final: 0.8414 (mt) REVERT: E 241 MET cc_start: 0.8023 (mmm) cc_final: 0.7706 (mmm) REVERT: E 242 LEU cc_start: 0.9025 (mp) cc_final: 0.8654 (mp) REVERT: E 245 SER cc_start: 0.8932 (t) cc_final: 0.8466 (p) REVERT: E 259 TYR cc_start: 0.9061 (t80) cc_final: 0.8528 (t80) REVERT: E 260 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8318 (tmmm) REVERT: E 263 MET cc_start: 0.8110 (mmm) cc_final: 0.7573 (tpp) REVERT: E 271 THR cc_start: 0.9139 (p) cc_final: 0.8767 (t) REVERT: E 292 SER cc_start: 0.8575 (m) cc_final: 0.8375 (t) REVERT: E 326 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7574 (mt-10) REVERT: E 329 TYR cc_start: 0.6873 (t80) cc_final: 0.6557 (t80) REVERT: E 365 ASP cc_start: 0.6248 (m-30) cc_final: 0.6002 (m-30) REVERT: F 5 ILE cc_start: 0.9191 (mt) cc_final: 0.8982 (mt) REVERT: F 15 TYR cc_start: 0.7884 (t80) cc_final: 0.7301 (t80) REVERT: F 18 LYS cc_start: 0.8014 (tppp) cc_final: 0.7689 (tppp) REVERT: F 26 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7245 (mm-30) REVERT: F 34 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8462 (ttmm) REVERT: F 43 HIS cc_start: 0.8694 (t-90) cc_final: 0.8223 (t-90) REVERT: F 60 LEU cc_start: 0.8815 (tp) cc_final: 0.8393 (tp) REVERT: F 61 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6509 (mm-30) REVERT: F 95 GLU cc_start: 0.7526 (tt0) cc_final: 0.7066 (tt0) REVERT: F 100 GLN cc_start: 0.8088 (mt0) cc_final: 0.7865 (mt0) REVERT: F 111 ILE cc_start: 0.8521 (mt) cc_final: 0.8304 (mm) REVERT: F 115 THR cc_start: 0.8728 (m) cc_final: 0.8136 (p) REVERT: F 119 LEU cc_start: 0.8491 (mt) cc_final: 0.8246 (mt) REVERT: F 146 PHE cc_start: 0.8275 (m-10) cc_final: 0.7494 (m-10) REVERT: F 157 ASP cc_start: 0.8504 (m-30) cc_final: 0.7880 (m-30) REVERT: F 166 MET cc_start: 0.8072 (ptm) cc_final: 0.7608 (tmm) REVERT: F 183 THR cc_start: 0.8136 (p) cc_final: 0.7709 (t) REVERT: F 200 ASN cc_start: 0.6997 (t0) cc_final: 0.6025 (t0) REVERT: F 237 ILE cc_start: 0.8896 (mm) cc_final: 0.7578 (mt) REVERT: F 256 TYR cc_start: 0.7558 (t80) cc_final: 0.7071 (t80) REVERT: F 263 MET cc_start: 0.7728 (mmm) cc_final: 0.7433 (tpp) REVERT: F 275 LEU cc_start: 0.8864 (tp) cc_final: 0.8478 (tt) REVERT: F 291 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7187 (mtt90) REVERT: F 296 GLU cc_start: 0.7420 (pt0) cc_final: 0.7212 (pt0) REVERT: F 329 TYR cc_start: 0.8045 (t80) cc_final: 0.7680 (t80) REVERT: F 340 ARG cc_start: 0.8858 (ttt-90) cc_final: 0.8634 (ttt-90) REVERT: F 345 GLU cc_start: 0.7935 (tt0) cc_final: 0.7334 (tt0) REVERT: F 419 MET cc_start: 0.3589 (mmp) cc_final: 0.3191 (tpt) REVERT: F 421 VAL cc_start: 0.7885 (t) cc_final: 0.7653 (p) REVERT: G 4 ILE cc_start: 0.9098 (mm) cc_final: 0.8820 (mm) REVERT: G 11 PHE cc_start: 0.8687 (m-80) cc_final: 0.8321 (m-80) REVERT: G 19 LEU cc_start: 0.8717 (mt) cc_final: 0.8387 (tt) REVERT: G 21 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7613 (mmtp) REVERT: G 35 PHE cc_start: 0.8475 (p90) cc_final: 0.8217 (p90) REVERT: G 46 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: G 47 GLN cc_start: 0.7793 (mt0) cc_final: 0.6225 (pt0) REVERT: G 77 TYR cc_start: 0.9066 (t80) cc_final: 0.8466 (t80) REVERT: G 80 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8420 (mm-30) REVERT: G 81 PHE cc_start: 0.8774 (m-80) cc_final: 0.8552 (m-80) REVERT: G 84 ASP cc_start: 0.9403 (p0) cc_final: 0.9199 (p0) REVERT: G 85 LEU cc_start: 0.9518 (mt) cc_final: 0.8847 (mm) REVERT: G 91 PHE cc_start: 0.9182 (t80) cc_final: 0.8528 (t80) REVERT: G 93 ILE cc_start: 0.9315 (tt) cc_final: 0.8939 (tt) REVERT: G 94 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7958 (tpp80) REVERT: G 95 LYS cc_start: 0.9328 (tttt) cc_final: 0.8626 (mtpp) REVERT: G 97 LYS cc_start: 0.8504 (tptm) cc_final: 0.8263 (mptm) REVERT: G 100 SER cc_start: 0.8467 (p) cc_final: 0.7850 (p) REVERT: G 194 PHE cc_start: 0.7795 (p90) cc_final: 0.7506 (p90) REVERT: G 210 ILE cc_start: 0.8876 (mm) cc_final: 0.8658 (mp) REVERT: G 231 TYR cc_start: 0.8867 (m-80) cc_final: 0.8409 (m-80) REVERT: G 238 ASP cc_start: 0.9241 (m-30) cc_final: 0.8544 (m-30) REVERT: G 243 GLU cc_start: 0.9412 (mp0) cc_final: 0.9179 (mp0) REVERT: G 263 ARG cc_start: 0.7843 (ptt180) cc_final: 0.7429 (ptt180) REVERT: G 265 VAL cc_start: 0.9017 (t) cc_final: 0.8128 (t) REVERT: G 266 TRP cc_start: 0.8438 (m100) cc_final: 0.7664 (m100) REVERT: G 295 ASP cc_start: 0.7469 (p0) cc_final: 0.5549 (p0) REVERT: G 304 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9013 (p) REVERT: G 305 ASN cc_start: 0.9068 (t0) cc_final: 0.8680 (t0) REVERT: G 307 MET cc_start: 0.9407 (mmt) cc_final: 0.8893 (mmm) REVERT: G 309 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8503 (mtp180) REVERT: G 310 LYS cc_start: 0.9309 (mttt) cc_final: 0.8912 (mmtm) REVERT: G 317 GLN cc_start: 0.9428 (mt0) cc_final: 0.9193 (mt0) REVERT: G 334 MET cc_start: 0.8127 (tpp) cc_final: 0.7567 (tpp) outliers start: 88 outliers final: 28 residues processed: 1336 average time/residue: 0.1982 time to fit residues: 396.0748 Evaluate side-chains 1159 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1123 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 116 ASN A 193 ASN A 219 HIS A 240 ASN A 295 ASN B 114 GLN C 45 ASN C 227 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 422 GLN F 48 HIS F 62 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101327 restraints weight = 48879.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104899 restraints weight = 25506.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107370 restraints weight = 15600.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109000 restraints weight = 10688.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110075 restraints weight = 8108.045| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 24515 Z= 0.196 Angle : 0.657 9.524 33269 Z= 0.342 Chirality : 0.045 0.306 3697 Planarity : 0.005 0.182 4105 Dihedral : 11.528 175.888 3510 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2917 helix: 1.31 (0.14), residues: 1443 sheet: -1.17 (0.27), residues: 376 loop : -1.18 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 36 TYR 0.031 0.002 TYR G 54 PHE 0.033 0.002 PHE G 293 TRP 0.019 0.002 TRP F 89 HIS 0.014 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00440 (24510) covalent geometry : angle 0.65219 (33263) hydrogen bonds : bond 0.04137 ( 1174) hydrogen bonds : angle 5.20186 ( 3363) metal coordination : bond 0.01588 ( 4) metal coordination : angle 5.97362 ( 6) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1216 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8394 (tpp) cc_final: 0.7886 (tpp) REVERT: A 3 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 11 PHE cc_start: 0.7813 (m-80) cc_final: 0.7437 (m-10) REVERT: A 19 VAL cc_start: 0.8155 (m) cc_final: 0.7858 (p) REVERT: A 26 GLU cc_start: 0.7943 (pm20) cc_final: 0.7464 (pm20) REVERT: A 29 GLU cc_start: 0.7691 (tt0) cc_final: 0.7317 (tt0) REVERT: A 35 ASN cc_start: 0.8583 (m-40) cc_final: 0.8206 (m110) REVERT: A 42 SER cc_start: 0.8609 (m) cc_final: 0.8288 (p) REVERT: A 47 TYR cc_start: 0.6396 (m-80) cc_final: 0.6075 (m-80) REVERT: A 60 LEU cc_start: 0.9175 (tp) cc_final: 0.8930 (tp) REVERT: A 73 VAL cc_start: 0.8918 (t) cc_final: 0.8223 (p) REVERT: A 79 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8087 (ttmt) REVERT: A 93 GLU cc_start: 0.8107 (tp30) cc_final: 0.7548 (tp30) REVERT: A 103 MET cc_start: 0.7715 (mmm) cc_final: 0.7380 (mmp) REVERT: A 113 ILE cc_start: 0.9025 (mt) cc_final: 0.8749 (mt) REVERT: A 123 LYS cc_start: 0.8263 (mmmm) cc_final: 0.8000 (mmmm) REVERT: A 131 VAL cc_start: 0.9023 (t) cc_final: 0.8694 (m) REVERT: A 146 PHE cc_start: 0.8376 (m-10) cc_final: 0.7869 (m-10) REVERT: A 163 LEU cc_start: 0.8802 (tp) cc_final: 0.8548 (tt) REVERT: A 166 MET cc_start: 0.7689 (mtm) cc_final: 0.7443 (mtm) REVERT: A 171 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7545 (mmtm) REVERT: A 174 PHE cc_start: 0.8645 (m-80) cc_final: 0.8214 (m-80) REVERT: A 214 TYR cc_start: 0.8465 (m-80) cc_final: 0.7536 (m-10) REVERT: A 215 LEU cc_start: 0.8598 (tp) cc_final: 0.8308 (tp) REVERT: A 224 ILE cc_start: 0.7447 (mt) cc_final: 0.6988 (mm) REVERT: A 235 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8136 (ttpt) REVERT: A 241 MET cc_start: 0.8136 (mmm) cc_final: 0.7605 (mmm) REVERT: A 255 SER cc_start: 0.8728 (p) cc_final: 0.8396 (p) REVERT: A 260 LYS cc_start: 0.8777 (tppt) cc_final: 0.8127 (tppt) REVERT: A 265 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8626 (ttpp) REVERT: A 267 ARG cc_start: 0.6917 (ttm-80) cc_final: 0.5353 (ttm-80) REVERT: A 268 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 312 TYR cc_start: 0.4677 (t80) cc_final: 0.4385 (t80) REVERT: A 313 LEU cc_start: 0.6932 (tt) cc_final: 0.6722 (tt) REVERT: A 316 CYS cc_start: 0.8128 (m) cc_final: 0.7663 (m) REVERT: A 371 ILE cc_start: 0.6510 (mt) cc_final: 0.6300 (mt) REVERT: A 380 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 384 MET cc_start: 0.8382 (ttt) cc_final: 0.7969 (ttm) REVERT: A 402 LYS cc_start: 0.7376 (ttpt) cc_final: 0.7099 (mmtt) REVERT: A 403 GLN cc_start: 0.8218 (tt0) cc_final: 0.7311 (tt0) REVERT: A 408 TYR cc_start: 0.8634 (m-80) cc_final: 0.8414 (m-80) REVERT: A 416 LYS cc_start: 0.8972 (mptt) cc_final: 0.8699 (mptt) REVERT: A 426 GLN cc_start: 0.8051 (mt0) cc_final: 0.7729 (mt0) REVERT: B 3 GLU cc_start: 0.7551 (tt0) cc_final: 0.6854 (tt0) REVERT: B 8 HIS cc_start: 0.8211 (m90) cc_final: 0.7432 (m90) REVERT: B 15 TYR cc_start: 0.8263 (t80) cc_final: 0.7801 (t80) REVERT: B 26 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 64 SER cc_start: 0.8669 (t) cc_final: 0.8388 (p) REVERT: B 79 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8144 (ttmm) REVERT: B 103 MET cc_start: 0.8010 (mmm) cc_final: 0.7592 (mmm) REVERT: B 139 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7638 (ttp-170) REVERT: B 144 ILE cc_start: 0.8941 (tt) cc_final: 0.8720 (tt) REVERT: B 145 SER cc_start: 0.8397 (p) cc_final: 0.7882 (p) REVERT: B 147 ASP cc_start: 0.7215 (m-30) cc_final: 0.6898 (m-30) REVERT: B 194 VAL cc_start: 0.8607 (t) cc_final: 0.8091 (t) REVERT: B 213 ASP cc_start: 0.7881 (m-30) cc_final: 0.7541 (m-30) REVERT: B 226 MET cc_start: 0.8176 (mmm) cc_final: 0.7496 (mmp) REVERT: B 231 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 243 ASP cc_start: 0.7368 (t0) cc_final: 0.6992 (t0) REVERT: B 245 SER cc_start: 0.8337 (t) cc_final: 0.8085 (t) REVERT: B 260 LYS cc_start: 0.8816 (tttp) cc_final: 0.8519 (tttp) REVERT: B 263 MET cc_start: 0.8024 (mmm) cc_final: 0.7719 (mmt) REVERT: B 265 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8616 (ttmt) REVERT: B 278 LYS cc_start: 0.8424 (tptp) cc_final: 0.8210 (tptp) REVERT: B 279 GLN cc_start: 0.8473 (tt0) cc_final: 0.8044 (tt0) REVERT: B 318 SER cc_start: 0.8159 (m) cc_final: 0.7384 (t) REVERT: B 324 TYR cc_start: 0.7507 (t80) cc_final: 0.7277 (t80) REVERT: B 368 MET cc_start: 0.8348 (tpp) cc_final: 0.7899 (ttt) REVERT: B 370 ASP cc_start: 0.7254 (m-30) cc_final: 0.6983 (m-30) REVERT: B 391 GLU cc_start: 0.7455 (tp30) cc_final: 0.7225 (tp30) REVERT: B 392 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 413 LYS cc_start: 0.8744 (tppt) cc_final: 0.8164 (tppt) REVERT: C 13 GLN cc_start: 0.7638 (tp40) cc_final: 0.7425 (tp40) REVERT: C 26 GLU cc_start: 0.8137 (pt0) cc_final: 0.7819 (pt0) REVERT: C 29 GLU cc_start: 0.7753 (tp30) cc_final: 0.7517 (tp30) REVERT: C 39 LEU cc_start: 0.8733 (mt) cc_final: 0.8383 (mt) REVERT: C 41 LYS cc_start: 0.8829 (tttt) cc_final: 0.8502 (tttt) REVERT: C 85 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7681 (mm-30) REVERT: C 114 GLN cc_start: 0.7742 (mt0) cc_final: 0.7436 (mt0) REVERT: C 155 MET cc_start: 0.7545 (tpt) cc_final: 0.7314 (tpt) REVERT: C 181 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8170 (ttpp) REVERT: C 203 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7585 (mtmm) REVERT: C 224 ILE cc_start: 0.7866 (mt) cc_final: 0.7633 (tp) REVERT: C 241 MET cc_start: 0.8184 (mmm) cc_final: 0.7456 (mmm) REVERT: C 243 ASP cc_start: 0.7720 (t0) cc_final: 0.7475 (t0) REVERT: C 263 MET cc_start: 0.7525 (mmm) cc_final: 0.7234 (mmm) REVERT: C 269 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7458 (mttm) REVERT: C 292 SER cc_start: 0.9106 (m) cc_final: 0.8759 (t) REVERT: C 312 TYR cc_start: 0.6597 (t80) cc_final: 0.6090 (t80) REVERT: C 333 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7563 (ttmt) REVERT: C 342 LEU cc_start: 0.9034 (tp) cc_final: 0.8753 (tp) REVERT: C 345 GLU cc_start: 0.8224 (tt0) cc_final: 0.7906 (tt0) REVERT: C 393 LEU cc_start: 0.8898 (mt) cc_final: 0.8626 (mt) REVERT: C 418 LEU cc_start: 0.8675 (mm) cc_final: 0.8431 (mm) REVERT: D 1 MET cc_start: 0.8046 (ppp) cc_final: 0.7317 (ppp) REVERT: D 29 GLU cc_start: 0.7184 (tt0) cc_final: 0.6964 (tt0) REVERT: D 35 ASN cc_start: 0.8730 (m110) cc_final: 0.8448 (m110) REVERT: D 41 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8131 (ttmm) REVERT: D 47 TYR cc_start: 0.9040 (m-80) cc_final: 0.8106 (m-80) REVERT: D 66 THR cc_start: 0.8133 (p) cc_final: 0.7596 (p) REVERT: D 89 TRP cc_start: 0.8130 (t60) cc_final: 0.7479 (t60) REVERT: D 93 GLU cc_start: 0.7907 (mm-30) cc_final: 0.6850 (mm-30) REVERT: D 96 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8047 (ttpp) REVERT: D 103 MET cc_start: 0.8020 (mmm) cc_final: 0.7257 (mmm) REVERT: D 118 GLU cc_start: 0.7546 (tp30) cc_final: 0.6899 (tp30) REVERT: D 139 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7786 (ttp-170) REVERT: D 143 SER cc_start: 0.8957 (m) cc_final: 0.8178 (t) REVERT: D 154 TRP cc_start: 0.8855 (t60) cc_final: 0.8355 (t60) REVERT: D 155 MET cc_start: 0.8080 (tpt) cc_final: 0.6942 (tpt) REVERT: D 189 THR cc_start: 0.8627 (p) cc_final: 0.7079 (p) REVERT: D 196 MET cc_start: 0.7562 (mtp) cc_final: 0.7265 (mtp) REVERT: D 226 MET cc_start: 0.7264 (mmm) cc_final: 0.6633 (mmm) REVERT: D 237 ILE cc_start: 0.8583 (mm) cc_final: 0.8363 (mm) REVERT: D 241 MET cc_start: 0.8325 (mmm) cc_final: 0.8077 (mtm) REVERT: D 263 MET cc_start: 0.7986 (mmm) cc_final: 0.7706 (mmm) REVERT: D 264 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8290 (mm-30) REVERT: D 324 TYR cc_start: 0.7787 (m-80) cc_final: 0.7337 (m-80) REVERT: D 326 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7213 (mm-30) REVERT: D 338 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6890 (mt-10) REVERT: D 347 GLU cc_start: 0.7771 (tp30) cc_final: 0.6959 (tp30) REVERT: D 349 VAL cc_start: 0.9126 (t) cc_final: 0.8910 (p) REVERT: D 392 GLU cc_start: 0.7742 (tp30) cc_final: 0.7512 (tp30) REVERT: D 397 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7847 (mt-10) REVERT: D 414 TRP cc_start: 0.8407 (m-90) cc_final: 0.8199 (m100) REVERT: D 416 LYS cc_start: 0.8166 (mppt) cc_final: 0.7354 (mppt) REVERT: E 1 MET cc_start: 0.8004 (ptm) cc_final: 0.6751 (ptm) REVERT: E 34 LYS cc_start: 0.8885 (tttp) cc_final: 0.8394 (tttp) REVERT: E 38 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8471 (mtpt) REVERT: E 39 LEU cc_start: 0.8887 (mt) cc_final: 0.8598 (mt) REVERT: E 47 TYR cc_start: 0.6406 (t80) cc_final: 0.6059 (t80) REVERT: E 79 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7904 (mtmt) REVERT: E 85 GLU cc_start: 0.7235 (mp0) cc_final: 0.6651 (mp0) REVERT: E 86 ASP cc_start: 0.8466 (t0) cc_final: 0.8036 (t70) REVERT: E 93 GLU cc_start: 0.8042 (tp30) cc_final: 0.7126 (tp30) REVERT: E 104 PHE cc_start: 0.8646 (t80) cc_final: 0.8170 (t80) REVERT: E 111 ILE cc_start: 0.9683 (mm) cc_final: 0.8952 (mm) REVERT: E 113 ILE cc_start: 0.9364 (mm) cc_final: 0.8093 (mm) REVERT: E 118 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7859 (mt-10) REVERT: E 126 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8484 (ptpt) REVERT: E 158 TYR cc_start: 0.5922 (p90) cc_final: 0.5683 (p90) REVERT: E 216 GLN cc_start: 0.8082 (mt0) cc_final: 0.7712 (mt0) REVERT: E 226 MET cc_start: 0.5934 (mmm) cc_final: 0.5526 (mmm) REVERT: E 228 MET cc_start: 0.7121 (ptm) cc_final: 0.6820 (ptm) REVERT: E 241 MET cc_start: 0.7933 (mmm) cc_final: 0.7480 (mmm) REVERT: E 246 LEU cc_start: 0.8854 (tp) cc_final: 0.8637 (tp) REVERT: E 247 ASP cc_start: 0.8123 (p0) cc_final: 0.7772 (p0) REVERT: E 248 ASP cc_start: 0.8056 (m-30) cc_final: 0.7834 (m-30) REVERT: E 260 LYS cc_start: 0.9021 (tptm) cc_final: 0.8734 (tptm) REVERT: E 263 MET cc_start: 0.8485 (mmm) cc_final: 0.8022 (tpp) REVERT: E 269 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8560 (ttmm) REVERT: E 271 THR cc_start: 0.9167 (p) cc_final: 0.8840 (t) REVERT: E 292 SER cc_start: 0.8172 (m) cc_final: 0.7885 (p) REVERT: E 296 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7236 (mt-10) REVERT: E 326 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7704 (mt-10) REVERT: E 333 LYS cc_start: 0.7825 (tttp) cc_final: 0.7434 (tttp) REVERT: E 402 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7237 (ttpp) REVERT: E 423 LYS cc_start: 0.9018 (mttm) cc_final: 0.8735 (mtpp) REVERT: F 5 ILE cc_start: 0.8993 (mt) cc_final: 0.8601 (mt) REVERT: F 15 TYR cc_start: 0.8644 (t80) cc_final: 0.7318 (t80) REVERT: F 22 TYR cc_start: 0.8211 (m-80) cc_final: 0.7987 (m-80) REVERT: F 24 ASP cc_start: 0.8524 (t70) cc_final: 0.8239 (t70) REVERT: F 29 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7639 (mm-30) REVERT: F 34 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8173 (ttmm) REVERT: F 38 LYS cc_start: 0.9135 (mmtp) cc_final: 0.8898 (mmtp) REVERT: F 43 HIS cc_start: 0.8455 (t-90) cc_final: 0.7841 (t-90) REVERT: F 60 LEU cc_start: 0.8703 (tp) cc_final: 0.8398 (tp) REVERT: F 61 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7401 (mm-30) REVERT: F 82 ASP cc_start: 0.7487 (t0) cc_final: 0.7278 (t0) REVERT: F 95 GLU cc_start: 0.8172 (tt0) cc_final: 0.7881 (tt0) REVERT: F 96 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8372 (ttpp) REVERT: F 116 ASN cc_start: 0.8743 (t0) cc_final: 0.8264 (t0) REVERT: F 119 LEU cc_start: 0.8619 (mt) cc_final: 0.8263 (mt) REVERT: F 123 LYS cc_start: 0.8809 (tptt) cc_final: 0.8447 (tptt) REVERT: F 155 MET cc_start: 0.6946 (tpp) cc_final: 0.5197 (tpp) REVERT: F 158 TYR cc_start: 0.7469 (p90) cc_final: 0.6558 (p90) REVERT: F 183 THR cc_start: 0.7954 (p) cc_final: 0.7389 (t) REVERT: F 184 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7726 (mmmt) REVERT: F 189 THR cc_start: 0.8231 (p) cc_final: 0.7714 (t) REVERT: F 235 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8264 (tttm) REVERT: F 236 ARG cc_start: 0.8459 (ttm170) cc_final: 0.8199 (tpp80) REVERT: F 237 ILE cc_start: 0.8930 (mm) cc_final: 0.7172 (mt) REVERT: F 256 TYR cc_start: 0.7617 (t80) cc_final: 0.6611 (t80) REVERT: F 291 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7306 (mtt90) REVERT: F 329 TYR cc_start: 0.7984 (t80) cc_final: 0.7649 (t80) REVERT: F 333 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8293 (ttpp) REVERT: F 338 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7011 (mm-30) REVERT: F 345 GLU cc_start: 0.7490 (tt0) cc_final: 0.7028 (tt0) REVERT: F 370 ASP cc_start: 0.7316 (m-30) cc_final: 0.6980 (m-30) REVERT: F 405 LYS cc_start: 0.7021 (tptp) cc_final: 0.6376 (tptp) REVERT: F 407 ARG cc_start: 0.7877 (tmm-80) cc_final: 0.7305 (tmm-80) REVERT: F 422 GLN cc_start: 0.7326 (mt0) cc_final: 0.7102 (mt0) REVERT: G 4 ILE cc_start: 0.8989 (mm) cc_final: 0.8096 (mm) REVERT: G 8 ASP cc_start: 0.8916 (m-30) cc_final: 0.8327 (m-30) REVERT: G 19 LEU cc_start: 0.8287 (mt) cc_final: 0.7963 (tt) REVERT: G 77 TYR cc_start: 0.8494 (t80) cc_final: 0.7976 (t80) REVERT: G 78 LEU cc_start: 0.9503 (mt) cc_final: 0.9222 (mt) REVERT: G 85 LEU cc_start: 0.9320 (mt) cc_final: 0.9068 (mt) REVERT: G 89 TYR cc_start: 0.8206 (t80) cc_final: 0.7936 (t80) REVERT: G 92 GLU cc_start: 0.8566 (tp30) cc_final: 0.8305 (tp30) REVERT: G 93 ILE cc_start: 0.9189 (tt) cc_final: 0.8363 (tt) REVERT: G 97 LYS cc_start: 0.8515 (tptm) cc_final: 0.8295 (mptm) REVERT: G 100 SER cc_start: 0.8634 (p) cc_final: 0.8139 (p) REVERT: G 147 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8659 (mmmt) REVERT: G 151 LYS cc_start: 0.8801 (ptpp) cc_final: 0.8547 (pttp) REVERT: G 238 ASP cc_start: 0.8718 (m-30) cc_final: 0.8291 (m-30) REVERT: G 266 TRP cc_start: 0.7705 (m100) cc_final: 0.7500 (m100) REVERT: G 303 ASP cc_start: 0.8081 (p0) cc_final: 0.7748 (p0) REVERT: G 314 THR cc_start: 0.8640 (p) cc_final: 0.8438 (t) REVERT: G 328 GLN cc_start: 0.6888 (tp40) cc_final: 0.6516 (tp40) REVERT: G 333 LYS cc_start: 0.9192 (tttp) cc_final: 0.8944 (tttp) REVERT: G 334 MET cc_start: 0.7956 (tpp) cc_final: 0.7548 (tpp) REVERT: G 335 ARG cc_start: 0.8381 (mtm180) cc_final: 0.7919 (mtm180) outliers start: 2 outliers final: 0 residues processed: 1217 average time/residue: 0.1641 time to fit residues: 300.5876 Evaluate side-chains 1091 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1090 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1701 > 50: distance: 35 - 51: 12.664 distance: 39 - 56: 7.811 distance: 45 - 51: 10.691 distance: 51 - 52: 6.432 distance: 52 - 53: 6.435 distance: 52 - 55: 28.485 distance: 53 - 54: 11.722 distance: 53 - 56: 11.332 distance: 56 - 57: 6.523 distance: 57 - 58: 3.718 distance: 57 - 60: 12.310 distance: 58 - 59: 5.421 distance: 58 - 70: 15.585 distance: 60 - 61: 10.972 distance: 61 - 62: 16.916 distance: 61 - 63: 10.220 distance: 62 - 64: 7.919 distance: 63 - 65: 13.633 distance: 63 - 66: 5.198 distance: 64 - 65: 11.439 distance: 65 - 67: 15.771 distance: 66 - 68: 16.409 distance: 67 - 69: 4.042 distance: 68 - 69: 7.425 distance: 70 - 71: 16.774 distance: 71 - 72: 17.740 distance: 71 - 74: 17.541 distance: 72 - 73: 15.605 distance: 72 - 78: 6.306 distance: 74 - 75: 10.355 distance: 75 - 76: 11.228 distance: 75 - 77: 13.945 distance: 78 - 79: 16.595 distance: 79 - 80: 17.823 distance: 79 - 82: 13.943 distance: 80 - 81: 13.371 distance: 80 - 84: 33.324 distance: 82 - 83: 18.186 distance: 84 - 85: 14.046 distance: 85 - 86: 26.069 distance: 86 - 87: 40.568 distance: 86 - 90: 17.622 distance: 88 - 89: 42.552 distance: 90 - 91: 20.586 distance: 91 - 92: 13.521 distance: 91 - 94: 16.583 distance: 92 - 93: 17.967 distance: 92 - 98: 9.983 distance: 94 - 95: 19.779 distance: 95 - 96: 38.120 distance: 95 - 97: 27.910 distance: 98 - 99: 29.674 distance: 99 - 100: 30.407 distance: 99 - 102: 8.654 distance: 100 - 105: 20.077 distance: 102 - 103: 16.248 distance: 102 - 104: 32.618 distance: 105 - 106: 21.553 distance: 106 - 107: 6.075 distance: 106 - 109: 31.375 distance: 107 - 108: 14.485 distance: 107 - 113: 17.406 distance: 108 - 127: 19.563 distance: 109 - 110: 12.511 distance: 110 - 111: 16.432 distance: 110 - 112: 22.597 distance: 113 - 114: 22.865 distance: 114 - 115: 41.641 distance: 114 - 117: 29.550 distance: 115 - 116: 39.960 distance: 115 - 121: 22.072 distance: 116 - 135: 27.566 distance: 117 - 118: 20.554 distance: 118 - 119: 13.626 distance: 119 - 120: 17.421 distance: 121 - 122: 19.742 distance: 122 - 123: 32.695 distance: 122 - 125: 9.845 distance: 123 - 124: 10.430 distance: 123 - 127: 23.839 distance: 125 - 126: 7.385