Starting phenix.real_space_refine on Sun Jun 8 01:23:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsr_38626/06_2025/8xsr_38626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsr_38626/06_2025/8xsr_38626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsr_38626/06_2025/8xsr_38626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsr_38626/06_2025/8xsr_38626.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsr_38626/06_2025/8xsr_38626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsr_38626/06_2025/8xsr_38626.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.101 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5777 2.51 5 N 1613 2.21 5 O 1700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9130 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4722 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 18, 'TRANS': 597} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.15, per 1000 atoms: 0.67 Number of scatterers: 9130 At special positions: 0 Unit cell: (69.056, 94.848, 148.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 5 15.00 Mg 2 11.99 O 1700 8.00 N 1613 7.00 C 5777 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=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 61.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid -1 through 10 removed outlier: 3.677A pdb=" N GLN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 30 removed outlier: 3.693A pdb=" N VAL A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 51 through 71 removed outlier: 3.928A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 99 removed outlier: 3.596A pdb=" N VAL A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.902A pdb=" N PHE A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.562A pdb=" N LEU A 128 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 153 removed outlier: 3.548A pdb=" N ILE A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.515A pdb=" N VAL A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 203 removed outlier: 3.719A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Proline residue: A 181 - end of helix removed outlier: 3.735A pdb=" N MET A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 220 through 238 removed outlier: 3.620A pdb=" N GLU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.506A pdb=" N ILE A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 293 removed outlier: 4.298A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 3.920A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.890A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.651A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 removed outlier: 3.584A pdb=" N ARG A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.586A pdb=" N VAL A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 removed outlier: 3.961A pdb=" N ALA A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 31 through 50 removed outlier: 3.620A pdb=" N THR B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 4.101A pdb=" N ARG B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.621A pdb=" N ASP B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 158 removed outlier: 3.547A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 4.043A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.515A pdb=" N ARG B 176 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 189 removed outlier: 3.606A pdb=" N GLN B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.678A pdb=" N LEU B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.956A pdb=" N THR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.544A pdb=" N VAL B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 262 removed outlier: 3.682A pdb=" N ARG B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.517A pdb=" N LYS B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.648A pdb=" N ALA B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 305 through 324 removed outlier: 3.526A pdb=" N TYR B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 324 " --> pdb=" O GLY B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.503A pdb=" N ALA B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 removed outlier: 4.567A pdb=" N LEU B 357 " --> pdb=" O MET B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 364 removed outlier: 4.685A pdb=" N SER B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 364' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.534A pdb=" N VAL B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.649A pdb=" N ALA B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 493 through 504 removed outlier: 3.511A pdb=" N ALA B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.034A pdb=" N HIS B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 543 Processing helix chain 'B' and resid 559 through 570 removed outlier: 3.513A pdb=" N LEU B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 removed outlier: 5.308A pdb=" N ALA A 339 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 353 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.605A pdb=" N GLY A 412 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP A 496 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 414 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A 364 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N SER A 527 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 366 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 363 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL A 540 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A 365 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 367 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP A 543 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.578A pdb=" N VAL A 397 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 467 through 470 removed outlier: 6.416A pdb=" N GLY B 468 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP B 552 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 470 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 420 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU B 596 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA B 421 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N MET B 598 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 423 " --> pdb=" O MET B 598 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 599 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1500 1.31 - 1.43: 2407 1.43 - 1.56: 5309 1.56 - 1.68: 9 1.68 - 1.80: 61 Bond restraints: 9286 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.74e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" CA ASP B 593 " pdb=" C ASP B 593 " ideal model delta sigma weight residual 1.523 1.459 0.065 1.34e-02 5.57e+03 2.32e+01 bond pdb=" C8 ATP A 601 " pdb=" N7 ATP A 601 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.09e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.329 0.045 1.00e-02 1.00e+04 2.06e+01 ... (remaining 9281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 12488 3.47 - 6.93: 146 6.93 - 10.40: 14 10.40 - 13.87: 4 13.87 - 17.33: 1 Bond angle restraints: 12653 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.54 17.33 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.90 12.93 1.00e+00 1.00e+00 1.67e+02 angle pdb=" N VAL A 218 " pdb=" CA VAL A 218 " pdb=" C VAL A 218 " ideal model delta sigma weight residual 113.71 104.05 9.66 9.50e-01 1.11e+00 1.03e+02 angle pdb=" N ARG A 430 " pdb=" CA ARG A 430 " pdb=" C ARG A 430 " ideal model delta sigma weight residual 111.71 99.89 11.82 1.34e+00 5.57e-01 7.78e+01 angle pdb=" C5 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 126.80 119.05 7.75 1.00e+00 1.00e+00 6.00e+01 ... (remaining 12648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 5481 35.50 - 71.00: 44 71.00 - 106.50: 6 106.50 - 142.00: 0 142.00 - 177.50: 1 Dihedral angle restraints: 5532 sinusoidal: 2130 harmonic: 3402 Sorted by residual: dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 122.50 177.50 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA LEU B 195 " pdb=" C LEU B 195 " pdb=" N LEU B 196 " pdb=" CA LEU B 196 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU B 376 " pdb=" C GLU B 376 " pdb=" N SER B 377 " pdb=" CA SER B 377 " ideal model delta harmonic sigma weight residual -180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1294 0.071 - 0.141: 213 0.141 - 0.212: 10 0.212 - 0.283: 2 0.283 - 0.353: 2 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA ALA B 414 " pdb=" N ALA B 414 " pdb=" C ALA B 414 " pdb=" CB ALA B 414 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA ASP B 593 " pdb=" N ASP B 593 " pdb=" C ASP B 593 " pdb=" CB ASP B 593 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE B 448 " pdb=" CA ILE B 448 " pdb=" CG1 ILE B 448 " pdb=" CG2 ILE B 448 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1518 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 87 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C GLY A 87 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY A 87 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS A 88 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 345 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO B 346 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 568 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C HIS B 568 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS B 568 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 569 " -0.013 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 68 2.56 - 3.14: 7553 3.14 - 3.73: 13923 3.73 - 4.31: 20853 4.31 - 4.90: 33796 Nonbonded interactions: 76193 Sorted by model distance: nonbonded pdb=" OG SER A 375 " pdb="MG MG A 602 " model vdw 1.972 2.170 nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O1B ADP B 701 " pdb="MG MG B 702 " model vdw 2.113 2.170 nonbonded pdb=" O1B ATP A 601 " pdb="MG MG A 602 " model vdw 2.125 2.170 nonbonded pdb=" NH2 ARG A 185 " pdb=" OE2 GLU A 233 " model vdw 2.208 3.120 ... (remaining 76188 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: 1.820 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.006 0.082 9286 Z= 0.317 Angle : 1.033 17.332 12653 Z= 0.677 Chirality : 0.052 0.353 1521 Planarity : 0.005 0.058 1615 Dihedral : 10.788 177.500 3342 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.67 % Favored : 92.07 % Rotamer: Outliers : 0.73 % Allowed : 2.09 % Favored : 97.17 % 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: -5.75 (0.17), residues: 1186 helix: -3.78 (0.12), residues: 751 sheet: -2.94 (0.60), residues: 60 loop : -3.52 (0.25), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 229 HIS 0.014 0.002 HIS A 337 PHE 0.027 0.002 PHE B 64 TYR 0.011 0.002 TYR B 517 ARG 0.009 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.25490 ( 438) hydrogen bonds : angle 9.65155 ( 1293) covalent geometry : bond 0.00603 ( 9286) covalent geometry : angle 1.03282 (12653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 251 time to evaluate : 0.992 Fit side-chains REVERT: A 81 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7299 (ttp-170) REVERT: A 198 ARG cc_start: 0.7453 (ttp-170) cc_final: 0.7135 (ttm170) REVERT: A 565 GLU cc_start: 0.8154 (tt0) cc_final: 0.7144 (mt-10) REVERT: B 32 ARG cc_start: 0.6494 (pmt100) cc_final: 0.5702 (ptm-80) REVERT: B 51 ILE cc_start: 0.8457 (tp) cc_final: 0.8157 (pt) REVERT: B 100 MET cc_start: 0.8786 (ttm) cc_final: 0.8373 (ttm) REVERT: B 194 GLN cc_start: 0.6745 (tt0) cc_final: 0.6518 (tm-30) REVERT: B 236 ARG cc_start: 0.7351 (ptm-80) cc_final: 0.7072 (mtm110) REVERT: B 288 GLN cc_start: 0.7623 (mt0) cc_final: 0.7350 (pt0) REVERT: B 392 GLU cc_start: 0.7935 (tt0) cc_final: 0.6963 (tm-30) REVERT: B 394 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7148 (mt-10) REVERT: B 590 ARG cc_start: 0.7881 (ptt90) cc_final: 0.7390 (ptp-170) outliers start: 7 outliers final: 1 residues processed: 256 average time/residue: 1.3046 time to fit residues: 356.9591 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 506 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 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 28 ASN A 130 GLN A 172 ASN A 187 GLN A 337 HIS ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 186 ASN B 338 GLN B 349 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112803 restraints weight = 10545.531| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.66 r_work: 0.2935 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9286 Z= 0.159 Angle : 0.726 10.414 12653 Z= 0.379 Chirality : 0.045 0.204 1521 Planarity : 0.006 0.054 1615 Dihedral : 9.777 167.696 1350 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.77 % Allowed : 10.89 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.20), residues: 1186 helix: -2.44 (0.16), residues: 742 sheet: -2.44 (0.61), residues: 62 loop : -3.07 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 15 HIS 0.011 0.001 HIS A 337 PHE 0.013 0.002 PHE B 336 TYR 0.016 0.002 TYR A 431 ARG 0.006 0.001 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 438) hydrogen bonds : angle 5.32665 ( 1293) covalent geometry : bond 0.00355 ( 9286) covalent geometry : angle 0.72609 (12653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.372 Fit side-chains REVERT: A 7 ARG cc_start: 0.8353 (ptt90) cc_final: 0.7809 (ttp80) REVERT: A 81 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7236 (ttp-170) REVERT: A 170 LEU cc_start: 0.8023 (tt) cc_final: 0.7597 (mt) REVERT: A 195 ARG cc_start: 0.7679 (ttm170) cc_final: 0.6899 (tpt170) REVERT: B 32 ARG cc_start: 0.6371 (pmt100) cc_final: 0.5133 (ptm-80) REVERT: B 125 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 194 GLN cc_start: 0.6968 (tt0) cc_final: 0.6134 (tm-30) REVERT: B 232 ARG cc_start: 0.7020 (ttp80) cc_final: 0.6510 (ptt180) REVERT: B 236 ARG cc_start: 0.7712 (ptm-80) cc_final: 0.7148 (mtm110) REVERT: B 273 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: B 392 GLU cc_start: 0.7940 (tt0) cc_final: 0.6764 (tm-30) REVERT: B 394 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7120 (mt-10) REVERT: B 418 SER cc_start: 0.7346 (t) cc_final: 0.6981 (p) REVERT: B 590 ARG cc_start: 0.7973 (ptt90) cc_final: 0.7417 (ptt-90) REVERT: B 602 ARG cc_start: 0.7618 (ptp-170) cc_final: 0.7335 (ptm160) outliers start: 36 outliers final: 18 residues processed: 183 average time/residue: 1.3770 time to fit residues: 271.0960 Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 186 ASN B 349 GLN B 568 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112339 restraints weight = 10662.741| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.66 r_work: 0.2912 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9286 Z= 0.150 Angle : 0.673 11.283 12653 Z= 0.347 Chirality : 0.044 0.204 1521 Planarity : 0.005 0.053 1615 Dihedral : 9.424 163.695 1350 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.77 % Allowed : 13.61 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.21), residues: 1186 helix: -1.67 (0.17), residues: 756 sheet: -2.03 (0.65), residues: 57 loop : -2.80 (0.27), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 15 HIS 0.003 0.001 HIS B 158 PHE 0.012 0.002 PHE B 509 TYR 0.015 0.001 TYR A 431 ARG 0.006 0.001 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 438) hydrogen bonds : angle 4.79435 ( 1293) covalent geometry : bond 0.00344 ( 9286) covalent geometry : angle 0.67294 (12653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.944 Fit side-chains REVERT: A 81 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7304 (ttp-170) REVERT: A 170 LEU cc_start: 0.8069 (tt) cc_final: 0.7698 (mt) REVERT: A 195 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7060 (tpt-90) REVERT: A 269 MET cc_start: 0.7611 (ttt) cc_final: 0.7254 (ttt) REVERT: A 409 SER cc_start: 0.8811 (t) cc_final: 0.8159 (p) REVERT: A 509 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7497 (mtp85) REVERT: A 539 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8462 (t) REVERT: B 32 ARG cc_start: 0.6432 (pmt100) cc_final: 0.5197 (ptm-80) REVERT: B 159 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8106 (mtp85) REVERT: B 194 GLN cc_start: 0.6957 (tt0) cc_final: 0.6100 (tm-30) REVERT: B 232 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6574 (ptt180) REVERT: B 236 ARG cc_start: 0.7669 (ptm-80) cc_final: 0.7131 (mtm110) REVERT: B 273 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: B 284 SER cc_start: 0.8368 (p) cc_final: 0.8005 (m) REVERT: B 392 GLU cc_start: 0.7947 (tt0) cc_final: 0.6696 (tp30) REVERT: B 394 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7192 (mt-10) REVERT: B 415 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 418 SER cc_start: 0.7105 (t) cc_final: 0.6842 (p) REVERT: B 498 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7396 (mp) REVERT: B 590 ARG cc_start: 0.8012 (ptt90) cc_final: 0.7464 (ptt-90) REVERT: B 602 ARG cc_start: 0.7691 (ptp-170) cc_final: 0.7387 (ptm160) outliers start: 36 outliers final: 17 residues processed: 183 average time/residue: 1.0931 time to fit residues: 215.0840 Evaluate side-chains 155 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111817 restraints weight = 10745.409| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.68 r_work: 0.2968 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9286 Z= 0.136 Angle : 0.636 9.910 12653 Z= 0.329 Chirality : 0.043 0.192 1521 Planarity : 0.004 0.048 1615 Dihedral : 9.149 163.522 1350 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.34 % Allowed : 12.88 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.22), residues: 1186 helix: -1.20 (0.18), residues: 766 sheet: -1.96 (0.66), residues: 57 loop : -2.53 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 15 HIS 0.003 0.001 HIS B 158 PHE 0.011 0.001 PHE B 509 TYR 0.013 0.001 TYR A 431 ARG 0.006 0.000 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 438) hydrogen bonds : angle 4.51082 ( 1293) covalent geometry : bond 0.00310 ( 9286) covalent geometry : angle 0.63554 (12653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 1.055 Fit side-chains REVERT: A 1 MET cc_start: 0.8363 (tpp) cc_final: 0.7984 (tpt) REVERT: A 48 LYS cc_start: 0.7301 (mptm) cc_final: 0.7060 (mmtp) REVERT: A 81 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7250 (ttp-170) REVERT: A 170 LEU cc_start: 0.7993 (tt) cc_final: 0.7688 (mt) REVERT: A 195 ARG cc_start: 0.7656 (ttm170) cc_final: 0.6876 (tpp-160) REVERT: A 269 MET cc_start: 0.7537 (ttt) cc_final: 0.7328 (ttt) REVERT: A 282 MET cc_start: 0.7813 (tpp) cc_final: 0.7564 (mmt) REVERT: A 409 SER cc_start: 0.8761 (t) cc_final: 0.8124 (p) REVERT: A 431 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: A 439 ASP cc_start: 0.8251 (m-30) cc_final: 0.7957 (m-30) REVERT: A 509 ARG cc_start: 0.7717 (mtp180) cc_final: 0.7445 (mtp85) REVERT: B 26 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7909 (ptm160) REVERT: B 32 ARG cc_start: 0.6360 (pmt100) cc_final: 0.5107 (ptm-80) REVERT: B 194 GLN cc_start: 0.6882 (tt0) cc_final: 0.6008 (tm-30) REVERT: B 232 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6636 (ptt180) REVERT: B 236 ARG cc_start: 0.7571 (ptm-80) cc_final: 0.7050 (mtm110) REVERT: B 272 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7174 (mtp85) REVERT: B 273 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: B 284 SER cc_start: 0.8311 (p) cc_final: 0.7968 (m) REVERT: B 347 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.5556 (tp) REVERT: B 357 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7416 (tp) REVERT: B 392 GLU cc_start: 0.7858 (tt0) cc_final: 0.6552 (tp30) REVERT: B 394 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 590 ARG cc_start: 0.8030 (ptt90) cc_final: 0.7447 (ptt-90) REVERT: B 594 LEU cc_start: 0.8053 (tp) cc_final: 0.7809 (tp) REVERT: B 602 ARG cc_start: 0.7664 (ptp-170) cc_final: 0.7247 (ptm160) outliers start: 51 outliers final: 24 residues processed: 183 average time/residue: 1.1602 time to fit residues: 227.6688 Evaluate side-chains 170 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 320 ASN A 428 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111051 restraints weight = 10766.791| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.67 r_work: 0.3114 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9286 Z= 0.145 Angle : 0.637 11.567 12653 Z= 0.327 Chirality : 0.043 0.184 1521 Planarity : 0.005 0.056 1615 Dihedral : 8.868 161.466 1350 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.71 % Allowed : 15.29 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.23), residues: 1186 helix: -0.84 (0.18), residues: 770 sheet: -1.85 (0.67), residues: 57 loop : -2.39 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 15 HIS 0.003 0.001 HIS B 158 PHE 0.012 0.001 PHE B 509 TYR 0.012 0.001 TYR A 431 ARG 0.005 0.001 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 438) hydrogen bonds : angle 4.38315 ( 1293) covalent geometry : bond 0.00337 ( 9286) covalent geometry : angle 0.63660 (12653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.969 Fit side-chains REVERT: A 81 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7767 (ttp-170) REVERT: A 120 ASN cc_start: 0.8307 (p0) cc_final: 0.8072 (p0) REVERT: A 170 LEU cc_start: 0.8284 (tt) cc_final: 0.8015 (mt) REVERT: A 195 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7585 (tpp-160) REVERT: A 282 MET cc_start: 0.8175 (tpp) cc_final: 0.7918 (mmt) REVERT: A 392 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 409 SER cc_start: 0.9031 (t) cc_final: 0.8461 (p) REVERT: A 439 ASP cc_start: 0.8233 (m-30) cc_final: 0.7993 (m-30) REVERT: A 487 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7784 (pp) REVERT: A 509 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7774 (mtp85) REVERT: B 26 ARG cc_start: 0.8470 (ptm160) cc_final: 0.8231 (ptm160) REVERT: B 32 ARG cc_start: 0.6763 (pmt100) cc_final: 0.5558 (ptm-80) REVERT: B 79 GLU cc_start: 0.8164 (mp0) cc_final: 0.7927 (mp0) REVERT: B 194 GLN cc_start: 0.6948 (tt0) cc_final: 0.6330 (tm-30) REVERT: B 232 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7047 (ptt180) REVERT: B 236 ARG cc_start: 0.7747 (ptm-80) cc_final: 0.7435 (mtm110) REVERT: B 272 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7434 (mtp85) REVERT: B 273 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: B 284 SER cc_start: 0.8454 (p) cc_final: 0.8174 (m) REVERT: B 304 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 347 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.5864 (tp) REVERT: B 392 GLU cc_start: 0.8171 (tt0) cc_final: 0.7124 (tp30) REVERT: B 394 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 498 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 578 THR cc_start: 0.8879 (t) cc_final: 0.8614 (m) REVERT: B 590 ARG cc_start: 0.8178 (ptt90) cc_final: 0.7753 (ptt-90) REVERT: B 602 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7765 (ptm160) outliers start: 45 outliers final: 25 residues processed: 177 average time/residue: 1.1476 time to fit residues: 217.9370 Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 72.0962 > 50: distance: 54 - 58: 34.621 distance: 58 - 59: 14.358 distance: 59 - 60: 14.793 distance: 59 - 62: 25.572 distance: 62 - 63: 68.741 distance: 63 - 64: 38.896 distance: 63 - 65: 57.674 distance: 66 - 67: 56.943 distance: 67 - 68: 40.780 distance: 67 - 70: 38.503 distance: 68 - 69: 56.155 distance: 70 - 72: 39.210 distance: 73 - 74: 39.363 distance: 74 - 77: 56.579 distance: 75 - 76: 41.115 distance: 77 - 78: 69.342 distance: 78 - 79: 56.371 distance: 79 - 80: 39.261 distance: 79 - 81: 40.750 distance: 82 - 83: 40.464 distance: 84 - 91: 40.297 distance: 86 - 87: 55.604 distance: 88 - 89: 56.784 distance: 88 - 90: 57.154 distance: 92 - 93: 41.279 distance: 97 - 98: 40.785 distance: 100 - 101: 56.443 distance: 104 - 105: 39.014 distance: 107 - 108: 38.916 distance: 107 - 110: 57.129 distance: 108 - 111: 40.208 distance: 111 - 112: 56.243 distance: 112 - 113: 39.873 distance: 112 - 115: 40.611 distance: 113 - 114: 40.960 distance: 115 - 116: 40.244 distance: 116 - 117: 41.198 distance: 116 - 118: 39.623 distance: 123 - 124: 57.240 distance: 125 - 131: 41.106 distance: 126 - 127: 55.251 distance: 126 - 129: 38.811 distance: 127 - 128: 41.132 distance: 127 - 132: 34.450 distance: 129 - 130: 40.289 distance: 130 - 131: 40.044